Molecular dynamics¶

Molecular dynamics (MD) can be used to simulate the evolution of a system in time.

See also

To perform a MD simulation, first select the corresponding Task:

Task MolecularDynamics

All aspects of the simulation can then be configured using the MolecularDynamics block.

MolecularDynamics
   AddMolecules
      AtomTemperature float
      ContactDistance float
      Coords float_list
      CoordsBox float_list
      CoordsSigma float_list
      DeviationAngle float
      Energy float
      EnergySigma float
      FractionalCoords float_list
      FractionalCoordsBox float_list
      FractionalCoordsSigma float_list
      Frequency integer
      MinDistance float
      MoleFraction float
      NumAttempts integer
      Rotate Yes/No
      StartStep integer
      StopStep integer
      System string
      Temperature float
      TemperatureSigma float
      Velocity float
      VelocityDirection float_list
      VelocitySigma float
   End
   ApplyForce
      Force float_list
      PerAtom Yes/No
      Region string
   End
   ApplyVelocity
      Components [X | Y | Z | XY | YZ | XZ | XYZ]
      Region string
      Velocity float_list
   End
   Barostat
      BulkModulus float
      ConstantVolume Yes/No
      Duration integer_list
      Equal [None | XYZ | XY | YZ | XZ]
      Pressure float_list
      Scale [XYZ | Shape | X | Y | Z | XY | YZ | XZ]
      Tau float
      Type [None | Berendsen | MTK]
   End
   BinLog
      BiasEnergy Yes/No
      BoostFactor Yes/No
      ConservedEnergy Yes/No
      Density Yes/No
      DipoleMoment Yes/No
      Hypertime Yes/No
      KineticEnergy Yes/No
      MaxBiasEnergy Yes/No
      MaxBoostFactor Yes/No
      PotentialEnergy Yes/No
      Pressure Yes/No
      PressureTensor Yes/No
      Step Yes/No
      Temperature Yes/No
      Time Yes/No
      TotalEnergy Yes/No
      Volume Yes/No
   End
   BondBoost
      Chain
         AtomNames string
         MaxDistances float_list
         MinDistances float_list
      End
      DistanceRestraint string
      Moving Yes/No
      NSteps integer
      NumInstances integer
      Units [Default | MD]
   End
   CRESTMTD
      AddEnergy Yes/No
      GaussianScaling
         ScaleGaussians Yes/No
         ScalingSlope float
      End
      Height float
      NGaussiansMax integer
      NSteps integer
      Region string
      RestartFile string
      Width float
   End
   CVHD
      Bias
         DampingTemp float
         Delta float
         Height float
      End
      ColVarBB
         at1
            region string
            symbol string
         End
         at2
            region string
            symbol string
         End
         cutoff float
         p integer
         rmax float
         rmin float
      End
      ColVarBM
         at1
            region string
            symbol string
         End
         at2
            region string
            symbol string
         End
         cutoff float
         p integer
         rmax float
         rmin float
      End
      Frequency integer
      MaxEvents integer
      StartStep integer
      StopStep integer
      WaitSteps integer
   End
   CalcPressure Yes/No
   Checkpoint
      Frequency integer
      WriteProperties Yes/No
   End
   CopyRestartTrajectory Yes/No
   CosineShear
      Acceleration float
      Enabled Yes/No
      FlowDirection float_list
      ProfileAxis [X | Y | Z]
   End
   Deformation
      LatticeVelocity # Non-standard block. See details.
         ...
      End
      LengthRate float_list
      LengthVelocity float_list
      Period float
      ScaleAtoms Yes/No
      StartStep integer
      StopStep integer
      StrainRate # Non-standard block. See details.
         ...
      End
      TargetLattice # Non-standard block. See details.
         ...
      End
      TargetLength float_list
      Type [Linear | Exponential | Sine | Cosine]
   End
   Gravity
      Acceleration float
   End
   HeatExchange
      HeatingRate float
      Method [Simple | HEX | eHEX]
      Sink
         AtomList integer_list
         Box
            Amax float
            Amin float
            Bmax float
            Bmin float
            Cmax float
            Cmin float
         End
         Region string
      End
      Source
         AtomList integer_list
         Box
            Amax float
            Amin float
            Bmax float
            Bmin float
            Cmax float
            Cmin float
         End
         Region string
      End
      StartStep integer
      StopStep integer
   End
   InitialVelocities
      File string
      RandomVelocitiesMethod [Exact | Boltzmann | Gromacs]
      Temperature float
      Type [Zero | Random | FromFile | Input]
      Values # Non-standard block. See details.
         ...
      End
   End
   MovingRestraints
      Change [Linear | Sine | Cosine]
      Distance
         Atom1 integer
         Atom2 integer
         EndValue float
         StartValue float
      End
      Erf
         ForceConstant float
         MaxForce float
      End
      GaussianWell
         Sigma float
         WellDepth float
      End
      Harmonic
         ForceConstant float
      End
      Hyperbolic
         ForceConstant float
         MaxForce float
      End
      Name string
      Period float
      RestraintType [None | Harmonic | Hyperbolic | Erf | GaussianWell]
      StartStep integer
      StopStep integer
   End
   NSteps integer
   Plumed
      Input # Non-standard block. See details.
         ...
      End
      Parallel
         nCoresPerGroup integer
         nGroups integer
         nNodesPerGroup integer
      End
   End
   Preserve
      AngularMomentum Yes/No
      CenterOfMass Yes/No
      Momentum Yes/No
   End
   Print
      System Yes/No
      Velocities Yes/No
   End
   ReactionBoost
      BondBreakingRestraints
         Erf
            ForceConstant float
            MaxForce float
         End
         GaussianWell
            Sigma float
            WellDepth float
         End
         Harmonic
            ForceConstant float
         End
         Hyperbolic
            ForceConstant float
            MaxForce float
         End
         Taper
            Enabled Yes/No
            MaxDistance float
            MinDistance float
         End
         Type [None | Harmonic | Hyperbolic | Erf | GaussianWell]
      End
      BondMakingRestraints
         Erf
            ForceConstant float
            MaxForce float
         End
         GaussianWell
            Sigma float
            WellDepth float
         End
         Harmonic
            ForceConstant float
         End
         Hyperbolic
            ForceConstant float
            MaxForce float
         End
         Type [None | Harmonic | Hyperbolic | Erf | GaussianWell]
      End
      BondedRestraints
         Harmonic
            ForceConstant float
         End
         Type [None | Harmonic]
      End
      Change [TargetCoordinate | Force | LogForce]
      InitialFraction float
      InterEquilibrationSteps integer
      MinBondChange float
      MinBondStrength float
      NSteps integer
      NonBondedRestraints
         Exponential
            Epsilon float
            Sigma float
         End
         Type [None | Exponential]
      End
      PreEquilibrationSteps integer
      RMSDRestraint
         Erf
            ForceConstant float
            MaxForce float
         End
         GaussianWell
            Sigma float
            WellDepth float
         End
         Harmonic
            ForceConstant float
         End
         Hyperbolic
            ForceConstant float
            MaxForce float
         End
         Type [None | Harmonic | Hyperbolic | Erf | GaussianWell]
      End
      Region string
      TargetSystem string
      Type [None | Pair | RMSD]
   End
   Reactor
      ForceConstant float
      MassScaled Yes/No
      NSteps integer
      Radius float
   End
   ReflectiveWall
      Axis float_list
      Region string
      Threshold float
   End
   Remap
      Type [None | Atoms]
   End
   RemoveMolecules
      Formula string
      Frequency integer
      SafeBox
         Amax float
         Amin float
         Bmax float
         Bmin float
         Cmax float
         Cmin float
         FractionalCoordsBox float_list
      End
      SinkBox
         Amax float
         Amin float
         Bmax float
         Bmin float
         Cmax float
         Cmin float
         FractionalCoordsBox float_list
      End
      StartStep integer
      StopStep integer
   End
   ReplicaExchange
      AllowWrongResults Yes/No
      EWMALength integer
      SwapFrequency integer
      TemperatureFactors float_list
      Temperatures float_list
      nReplicas integer
   End
   Restart string
   Shake
      All string
      ConvergeR2 float
      ConvergeRV float
      Iterations integer
      ShakeInitialCoordinates Yes/No
   End
   Thermostat
      BerendsenApply [Local | Global]
      ChainLength integer
      Duration integer_list
      Region string
      Tau float
      Temperature float_list
      Type [None | Berendsen | NHC]
   End
   TimeStep float
   Trajectory
      ExitConditionFreq integer
      PrintFreq integer
      SamplingFreq integer
      TProfileGridPoints integer
      WriteBonds Yes/No
      WriteCharges Yes/No
      WriteCoordinates Yes/No
      WriteEngineGradients Yes/No
      WriteMolecules Yes/No
      WriteVelocities Yes/No
   End
   fbMC
      Frequency integer
      MassRoot float
      MolecularMoves
         Enabled Yes/No
         RotationStepAngle float
         TranslationStepLength float
      End
      NSteps integer
      PrintFreq integer
      StartStep integer
      StepLength float
      StopStep integer
      Temperature float
   End
End

General¶

The time evolution of the system is simulated by numerically integrating the equations of motion. A velocity Verlet integrator is used with a time step set by the TimeStep key. The MD driver will perform NSteps timesteps in total.

Because the overall computational cost depends on NSteps but not on TimeStep, it is desirable to set the timestep as large as possible to maximize the sampled timescale with a given computational budget. However, numerical integration errors grow rapidly as the timestep increases. These errors will cause a loss of energy conservation, crashes, and other artifacts. It is thus important to set the TimeStep value carefully, as its optimal value strongly depends on the studied system and simulated conditions.

As a rule of thumb, reasonable timesteps for systems not undergoing chemical reactions are 10-20 times lower than the period of the fastest vibration mode. Systems containing hydrogen atoms at room temperature can thus be accurately simulated using a 1 fs timestep. Longer timesteps can be safely used for systems containing only heavy atoms (vibration periods scale with the square root of the atomic mass). Conversely, the timestep needs to be made shorter for high-temperature simulations. The same also applies to simulations of chemical reactions, which are usually accompanied by significant transient local heating. The default timestep of 0.25 fs should work for most of these cases.

MolecularDynamics

NSteps

Type: Integer
Default value: 1000
GUI name: Number of steps
Description: The number of steps to be taken in the MD simulation.

TimeStep

Type: Float
Default value: 0.25
Unit: Femtoseconds
Description: The time difference per step.

During a long simulation, numerical integration errors will cause some system-wide quantities to drift from their exact values. For example, the system may develop a nonzero net linear velocity, causing an overall translation or flow. Non-periodic (molecular) and 1D-periodic systems may also develop nonzero angular momentum (overall rotation) and a Brownian motion of their center of mass through space. These problems are corrected by periodically removing any accumulated drift. This feature can be controlled using the Preserve key.

MolecularDynamics

Preserve

Type: Block
Description: Periodically remove numerical drift accumulated during the simulation to preserve different whole-system parameters.

AngularMomentum

Type: Bool
Default value: Yes
GUI name: : Angular momentum
Description: Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems, and disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).

CenterOfMass

Type: Bool
Default value: No
GUI name: : Center of mass
Description: Translate the system to keep its center of mass at the coordinate origin. This option is not very useful for 3D-periodic systems.

Momentum

Type: Bool
Default value: Yes
GUI name: Preserve: Total momentum
Description: Remove overall (linear) momentum of the system. This is disabled by default for systems which are not translationally invariant (for example when frozen atoms are present).

Constrained molecular dynamics¶

There are two types of constraint available for MD: frozen atoms and Shake/Rattle. Atoms can be kept frozen using the Atom, AtomList and FixedRegion keys of the Constraints top-level input block.

Constraints

Atom

Type: Integer
Recurring: True
Description: Fix the position of an atom. Just one integer referring to the index of the atom in the [System%Atoms] block.

AtomList

Type: Integer List
Recurring: True
Description: Fix positions of the specified atoms. A list of integers referring to indices of atoms in the [System%Atoms] block.

FixedRegion

Type: String
Recurring: True
Description: Fix positions of all atoms in a region.

The Shake/Rattle constraints are implemented following H.C. Andersen, J Comp. Phys., 52 (1983) 24. The procedure consists of two steps: update of the coordinates to satisfy the constraints (the Shake part) and orthogonalization of atomic velocities to them (the Rattle part). The Shake part is implemented as an additional correcting force that brings each bond length exactly to its constrained value upon the subsequent velocity Verlet integration step. Application of the constraints is an iterative procedure and the convergence greatly depends on how intertwined the constraints are. For diatomic molecules, usually no more than two iterations are necessary, while tens of iterations may be required for rings (a triangle constraint is treated as a 3-membered ring).

Note

During simulations with a changing simulation box (NpT, NpH), the absolute Cartesian coordinates of the frozen atoms cannot be kept fixed. In this case, their fractional cell coordinates are maintained at the original values. Also the Shake constraints cannot be satisfied exactly during such simulations but the difference is usually small enough.

The Shake/Rattle constraints are specified using the Shake input block:

MolecularDynamics

Shake

Type: Block
Description: Parameters of the Shake/Rattle algorithm.

All

Type: String
Recurring: True
GUI name: Constrain all
Description: Constraint description in one the following formats: All [bondOrder] bonds at1 at2 [to distance] All triangles at1 at2 at3 The first option constrains all bonds between atoms at1 at2 to a certain length, while the second - bonds at1-at2 and at2-at3 and the angle between them. The [bondOrder] can be a number or a string such as single, double, triple or aromatic. If it’s omitted then all bonds between specified atoms will be constrained. Atom names are case-sensitive and they must be as they are in the Atoms block, or an asterisk ‘*’ denoting any atom. The distance, if present, must be in Angstrom. If it is omitted then the bond length from the initial geometry is used. Important: only the bonds present in the system at certain points of the simulation (at the start or right after adding/removing atoms) can be constrained, which means that the bonds may need to be specified in the System block. Warning: the triangles constraint should be used with care because each constrained bond or angle means removing one degree of freedom from the dynamics. When there are too many constraints (for example, “All triangles H C H” in methane) some of them may be linearly dependent, which will lead to an error in the temperature computation. Valid examples: All single bonds C C to 1.4 All bonds O H to 0.98 All bonds O H All bonds H * All triangles H * H

ConvergeR2

Type: Float
Default value: 1e-08
Description: Convergence criterion on the max squared difference, in atomic units.

ConvergeRV

Type: Float
Default value: 1e-08
Description: Convergence criterion on the orthogonality of the constraint and the relative atomic velocity, in atomic units.

Iterations

Type: Integer
Default value: 100
Description: Number of iterations.

ShakeInitialCoordinates

Type: Bool
Default value: Yes
Description: Apply constraints before computing the first energy and gradients.

Note

The list of constrained bonds is built by matching the input against the bonds as specified in the System block. This means that bonds not specified in the System block will not be constrained.

(Re-)Starting a simulation¶

The state of a system at the beginning of a simulation is defined by the positions and momenta of all atoms. The positions can be set in the input or loaded from a file as described under Geometry, System definition. Initial velocities are then supplied using the InitialVelocities block.

Probably the most common way to start up a simulation is to draw the initial velocities from a Maxwell-Boltzmann distribution by setting Type=Random and Temperature to a suitable value. Alternatively, velocities can be loaded from an ams.rkf file produced by an earlier simulation using Type=FromFile and File. This is the recommended way to start a production simulation from the results of a short preparation/equilibration run.

Velocities of all atoms in units of Å/fs can also be explicitly defined in the Values block after setting Type=Input. This is mainly useful to repeat or extend simulations done by other programs. For example, velocities can be extracted from the vels or moldyn.vel files used by the standalone ReaxFF program. A simple AWK script is supplied in scripting/standalone/reaxff-ams/vels2ams.awk to help with the conversion.

MolecularDynamics

InitialVelocities

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

File

Type: String
Description: AMS RKF file containing the initial velocities.

RandomVelocitiesMethod

Type: Multiple Choice
Default value: Exact
Options: [Exact, Boltzmann, Gromacs]
GUI name: Velocity randomization method
Description: Specifies how are random velocities generated. Three methods are available. Exact: Velocities are scaled to exactly match set random velocities temperature. Boltzmann: Velocities are not scaled and sample Maxwell-Boltzmann distribution. However, the distribution is not corrected for constraints. Gromacs: Velocities are scaled to match set random velocities temperature, but removal of net momentum is performed only after the scaling. Resulting kinetic energy is lower based on how much net momentum the system had.

Temperature

Type: Float
Unit: Kelvin
GUI name: Initial temperature
Description: Sets the temperature for the Maxwell-Boltzmann distribution when the type of the initial velocities is set to random, in which case specifying this key is mandatory. AMSinput will use the first temperature of the first thermostat as default.

Type

Type: Multiple Choice
Default value: Random
Options: [Zero, Random, FromFile, Input]
GUI name: Initial velocities
Description: Specifies the initial velocities to assign to the atoms. Three methods to assign velocities are available. Zero: All atom are at rest at the beginning of the calculation. Random: Initial atom velocities follow a Maxwell-Boltzmann distribution for the temperature given by the [MolecularDynamics%InitialVelocities%Temperature] keyword. FromFile: Load the velocities from a previous ams result file. Input: Atom’s velocities are set to the values specified in the [MolecularDynamics%InitialVelocities%Values] block, which can be accessed via the Expert AMS panel in AMSinput.

Values

Type: Non-standard block
Description: This block specifies the velocity of each atom, in Angstrom/fs, when [MolecularDynamics%InitialVelocities%Type] is set to Input. Each row must contain three floating point values (corresponding to the x,y,z component of the velocity vector) and a number of rows equal to the number of atoms must be present, given in the same order as the [System%Atoms] block.

The MD module also supports exact restarts of interrupted simulations by pointing the Restart key to an ams.rkf file. This will restore the entire state of the MD module from the last available checkpoint (if the previous simulation was interrupted) or from the final state (if the previous simulation ended after NSteps). An earlier trajectory can thus be seamlessly extended by increasing NSteps and using Restart.

Note

Restart should be combined with LoadSystem from the same ams.rkf to restore the atomic positions.

Warning

The Restart feature is only intended for exact restarts, so the rest of the MolecularDynamics settings should be the same as in the original run. Only NSteps and engine settings (contents of the Engine block) can always be changed safely across restarts.

Although some MD settings (such as the trajectory sampling options) can in practice be changed without problems, changing others (such as thermostat or barostat settings) will cause the restart to fail or produce physically incorrect results. It is thus strongly recommended to only use Restart for exact continuation and InitialVelocities Type=FromFile together with LoadSystem otherwise.

MolecularDynamics

Restart

Type: String
GUI name: Restart from
Description: The path to the ams.rkf file from which to restart the simulation.

Thermostats and barostats¶

By default, the MD simulation samples the microcanonical (NVE) ensemble. Although this is useful to check energy conservation and other basic physical properties, it does not directly map to common experimental conditions. The canonical (NVT) ensemble can be sampled instead by applying a Thermostat, which serves as a simulated heat bath around the system, keeping its average temperature at a set value.

AMS offers two thermostats with drastically different properties, mode of operation, and applicability, selected using the Type key:

Berendsen

The Berendsen friction thermostat drives the system to a particular target temperature by rescaling the velocities of all atoms in each step. This ensures rapid (exponential) convergence of the temperature with a time constant Tau. However, this thermostat produces an incorrect velocity distribution and should thus be avoided in all situations where correct energy fluctuations are important. Additionally, using a too short time constant Tau tends to cause incorrect equipartition of energy between different degrees of freedom in the system, leading to the “flying ice cube” phenomenon. The time constant Tau should thus be set as large as possible to limit these artifacts while still providing sufficient temperature control. Common values of Tau for condensed-phase systems lie between 100 fs (strong damping, rapid convergence) and 10 ps (weak coupling with minimal artifacts).

This thermostat is mainly useful for systems far from equilibrium, for example during the initial preparation and equilibration phase of a simulation. The NHC thermostat should be preferred where possible.

NHC

This enables a chain of coupled Nosé-Hoover thermostats. This method introduces artificial degrees of freedom representing the heat bath and ensures correct sampling of the canonical ensemble. The combined total energy of the system and the heat bath is conserved and shown in the GUI as Conserved Energy. Checking this quantity for drift and artifacts thus offers a valuable test of the correctness of the simulation. This thermostat exhibits oscillatory relaxation with a period of Tau. It is thus not well suited for systems starting far from equilibrium, because the oscillations may take long to settle. The time constant Tau should be at least comparable to the period of some natural oscillation of the system to ensure efficient energy transfer. It is commonly on the order of hundreds of femtoseconds, although higher values may be used if weak coupling is desired.

Multiple independent thermostats can be used to separately control different non-overlapping regions of the system at the same time. This is done by first defining appropriate Regions in the System block and then specifying the Thermostat block multiple times with the Region key of each thermostat set to an appropriate region expression.

MolecularDynamics

Thermostat

Type: Block
Recurring: True
Description: This block allows to specify the use of a thermostat during the simulation. Depending on the selected thermostat type, different additional options may be needed to characterize the specific thermostat’ behavior.

BerendsenApply

Type: Multiple Choice
Default value: Global
Options: [Local, Global]
GUI name: Apply Berendsen
Description: Select how to apply the scaling correction for the Berendsen thermostat: - per-atom-velocity (Local) - on the molecular system as a whole (Global).

ChainLength

Type: Integer
Default value: 10
GUI name: NHC chain length
Description: Number of individual thermostats forming the NHC thermostat

Duration

Type: Integer List
GUI name: Duration(s)
Description: Specifies how many steps should a transition from a particular temperature to the next one in sequence take.

Region

Type: String
Default value: *
Description: The identifier of the region to thermostat. The default ‘*’ applies the thermostat to the entire system. The value can by a plain region name, or a region expression, e.g. ‘*-myregion’ to thermostat all atoms that are not in myregion, or ‘regionA+regionB’ to thermostat the union of the ‘regionA’ and ‘regionB’. Note that if multiple thermostats are used, their regions may not overlap.

Tau

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: The time constant of the thermostat.

Temperature

Type: Float List
Unit: Kelvin
GUI name: Temperature(s)
Description: The target temperature of the thermostat. You can specify multiple temperatures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one T to the next T (using a linear ramp). For NHC thermostat, the temperature may not be zero.

Type

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, NHC]
GUI name: Thermostat
Description: Selects the type of the thermostat.

Just like using a Thermostat to control the temperature of the system, a Barostat can be applied to keep the pressure constant by adjusting the volume. This enables sampling the isenthalpic-isobaric (NpH) ensemble by using only a barostat or the isothermal-isobaric (NpT) ensemble by combining a barostat and a thermostat. Unlike thermostats, a barostat always applies to the entire system and there can thus be at most one barostat defined.

AMS offers two barostats with similar properties to the related thermostats:

Berendsen: The Berendsen friction-like isobaric ensemble method rescales the system in each step to drive the pressure towards a target value. Similarly to the Berendsen thermostat, the relaxation is exponential with a time constant Tau. Similar considerations for the choice of Tau apply as in the case of the thermostat, but the value of Tau for the barostat is usually at least several times higher than the corresponding Tau used for the thermostat. This barostat does not have any conserved quantity.
MTK: This enables the Martyna-Tobias-Klein extended Lagrangian barostat, which generates a true isobaric ensemble by integrating the cell parameters as additional degrees of freedom. This barostat is derived from the Andersen-Hoover isotropic barostat and the Parrinello-Rahman-Hoover anisotropic barostat. Like the NHC thermostat, it exhibits oscillatory relaxation unsuitable for systems far from equilibrium. This barostat must always be combined with a NHC thermostat. One instance of such thermostat coupled to the atoms as usual, while a second instance is created internally and coupled to the cell degrees of freedom.

MolecularDynamics

Barostat

Type: Block
Description: This block allows to specify the use of a barostat during the simulation.

BulkModulus

Type: Float
Default value: 2200000000.0
Unit: Pascal
Description: An estimate of the bulk modulus (inverse compressibility) of the system for the Berendsen barostat. This is only used to make Tau correspond to the true observed relaxation time constant. Values are commonly on the order of 10-100 GPa (1e10 to 1e11) for solids and 1 GPa (1e9) for liquids (2.2e9 for water). Use 1e9 to match the behavior of standalone ReaxFF.

ConstantVolume

Type: Bool
Default value: No
Description: Keep the volume constant while allowing the box shape to change. This is currently supported only by the MTK barostat.

Duration

Type: Integer List
Description: Specifies how many steps should a transition from a particular pressure to the next one in sequence take.

Equal

Type: Multiple Choice
Default value: None
Options: [None, XYZ, XY, YZ, XZ]
Description: Enforce equal scaling of the selected set of dimensions. They will be barostatted as one dimension according to the average pressure over the components.

Pressure

Type: Float List
Unit: Pascal
Description: Specifies the target pressure. You can specify multiple pressures (separated by spaces). In that case the Duration field specifies how many steps to use for the transition from one p to the next p (using a linear ramp).

Scale

Type: Multiple Choice
Default value: XYZ
Options: [XYZ, Shape, X, Y, Z, XY, YZ, XZ]
Description: Dimensions that should be scaled by the barostat to maintain pressure. Selecting Shape means that all three dimensions and also all the cell angles are allowed to change.

Tau

Type: Float
Unit: Femtoseconds
GUI name: Damping constant
Description: Specifies the time constant of the barostat.

Type

Type: Multiple Choice
Default value: None
Options: [None, Berendsen, MTK]
GUI name: Barostat
Description: Selects the type of the barostat.

Temperature and pressure regimes¶

Arbitrary temperature and pressure regimes can be generated by setting Temperature or Pressure to a list of values, corresponding to the successive set points. This needs to be accompanied by a Duration key specifying the length of each regime segment in steps:

Thermostat
   Temperature 0     300     300     500     500     300
   Duration      100     200     100     200     100
End

Note that there is always N-1 Duration values for N Temperature values. The target temperature of the thermostat in this example will evolve as follows:

Increase linearly from 0 to 300 K over 100 steps.
Stay constant at 300 K for 200 steps.
Increase linearly from 300 to 500 K over 100 steps.
Stay constant at 500 K for 200 steps.
Decrease linearly from 500 to 300 K over 100 steps.
Stay constant at 300 K for the rest of the simulation.

Trajectory sampling and output¶

A basic principle of the numerical integration of motion in MD is that the changes in the state of the system between successive time steps are small. This means that storing the results of every step is not useful, because all the data is strongly correlated. Instead, a snapshot of the system is taken every N steps, where N is set low enough to still capture the fastest motion of interest but high enough to avoid wasting space due to correlations. The resulting sequence of snapshots is then commonly called the trajectory.

AMS writes the trajectory to the History and MDHistory sections of ams.rkf, according to the settings in the Trajectory block. A snapshot of the system and various MD variables is stored every SamplingFreq timesteps. By default, this frequency is also used to print basic thermodynamic parameters of the simulation to the output and log file. Set PrintFreq to override this.

Frequently sampling a long trajectory can generate large volumes of data. If the space usage becomes a concern, one can selectively disable storing some parts of the trajectory to save space using the Write* keys. Note however that this will make it impossible to use some analysis methods on the resulting trajectory:

WriteBonds is necessary for reaction network analysis (ChemTraYzer). Disabling WriteBonds also makes AMSmovie show only guessed bonds instead of those calculated by the engine.
WriteMolecules is required by the Molecule Fractions panel in AMSmovie.
WriteVelocities is required to calculate the velocity autocorrelation functions needed for diffusivity and IR spectra.

The trajectory itself contains only the data needed for subsequent analysis of the dynamics of the system. However, much more data is usually generated on every integration step. This includes, for example, the internal data used by an engine when evaluating the energies and forces. This information is normally discarded after each step, because it is often very large. However, a Checkpoint containing the complete internal state of the MD driver together with a result file generated by the engine is stored every Frequency steps. An interrupted simulation can then be restarted from this checkpoint using the Restart keyword. Additionally, the engine result files called MDStep*.rkf can also be used to extract various engine-specific details about the system, such as the orbitals for QM engines.

MolecularDynamics

Trajectory

Type: Block
Description: Sets the frequency for printing to stdout and storing the molecular configuration on the .rkf file.

ExitConditionFreq

Type: Integer
GUI name: Exit condition frequency
Description: Check the exit conditions every N steps. By default this is done every SamplingFreq steps.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N steps. By default this is done every SamplingFreq steps.

SamplingFreq

Type: Integer
Default value: 100
GUI name: Sample frequency
Description: Write the the molecular geometry (and possibly other properties) to the .rkf file once every N steps.

TProfileGridPoints

Type: Integer
Default value: 0
Description: Number of points in the temperature profile. If TProfileGridPoints > 0, a temperature profile along each of the three lattice axes will be written to the .rkf file. The temperature at a given profile point is calculated as the total temperature of all atoms inside the corresponding slice of the simulation box, time-averaged over all MD steps since the previous snapshot. By default, no profile is generated.

WriteBonds

Type: Bool
Default value: Yes
Description: Write detected bonds to the .rkf file.

WriteCharges

Type: Bool
Default value: Yes
Description: Write current atomic point charges (if available) to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze charges.

WriteCoordinates

Type: Bool
Default value: Yes
Description: Write atomic coordinates to the .rkf file.

WriteEngineGradients

Type: Bool
Default value: No
Description: Write atomic gradients (negative of the atomic forces, as calculated by the engine) to the History section of ams.rkf.

WriteMolecules

Type: Bool
Default value: Yes
Description: Write the results of molecule analysis to the .rkf file.

WriteVelocities

Type: Bool
Default value: Yes
Description: Write velocities to the .rkf file. Disable this to reduce trajectory size if you do not need to analyze the velocities.

Checkpoint

Type: Block
Description: Sets the frequency for storing the entire MD state necessary for restarting the calculation.

Frequency

Type: Integer
Default value: 1000
GUI name: Checkpoint frequency
Description: Write the MD state and engine-specific data to the respective .rkf files once every N steps.

WriteProperties

Type: Bool
Default value: No
Description: Write the properties from the properties section to the ChecoPoint file once every N steps.

CalcPressure

Type: Bool
Default value: No
GUI name: Calculate pressure
Description: Calculate the pressure in periodic systems. This may be computationally expensive for some engines that require numerical differentiation. Some other engines can calculate the pressure for negligible additional cost and will always do so, even if this option is disabled.

Print

Type: Block
Description: This block controls the printing of additional information to stdout.

System

Type: Bool
Default value: No
Description: Print the chemical system before and after the simulation.

Velocities

Type: Bool
Default value: No
Description: Print the atomic velocities before and after the simulation.

In rare cases, one may require some properties from every MD step, for example, the pressure tensor for the Green-Kubo viscosity calculation. In this case one can use the BinLog (binary log) feature. When enabled, the selected MD variables will be stored in the BinLog section of ams.rkf in the format similar to that of the MDHistory section with a few differences: the blocking factor is larger (1000 instead of 100) and the pressure tensor is stored per component, for example, P_xx is stored in PressureTensor_xx, and so on. Note that none of the atomic properties (coordinates, velocities) are included in the binlog.

MolecularDynamics

BinLog

Type: Block
Description: This block controls writing the BinLog section in ams.rkf, which contains the selected MD state scalars and tensors from every MD step. No per-atom data is written. If you need the per-atom data then you can set the sampling frequency to 1 and get the required data from the MDHistory section. The tensors are written per component, that is, the pressure tensor is written as six variables: PressureTensor_xx, PressureTensor_yy, etc.. To reduce the file size, all data is written in blocks.

BiasEnergy

Type: Bool
Default value: No
Description: Write the CVDH bias energy.

BoostFactor

Type: Bool
Default value: No
Description: Write the CVDH boost factor.

ConservedEnergy

Type: Bool
Default value: No
Description: Write the conserved energy value.

Density

Type: Bool
Default value: No
Description: Write the density.

DipoleMoment

Type: Bool
Default value: No
Description: Write the dipole moment. Each component of the tensor is written in its own variable.

Hypertime

Type: Bool
Default value: No
Description: Write the CVDH hypertime.

KineticEnergy

Type: Bool
Default value: No
Description: Write the kinetic energy value.

MaxBiasEnergy

Type: Bool
Default value: No
Description: Write the max CVDH bias energy.

MaxBoostFactor

Type: Bool
Default value: No
Description: Write the max CVDH boost factor.

PotentialEnergy

Type: Bool
Default value: No
Description: Write the potential energy value.

Pressure

Type: Bool
Default value: No
Description: Write the pressure.

PressureTensor

Type: Bool
Default value: No
Description: Write the pressure tensor in Voigt notation. Each component of the tensor is written in its own variable.

Step

Type: Bool
Default value: No
Description: Write the step index during the simulation.

Temperature

Type: Bool
Default value: No
Description: Write the temperature.

Time

Type: Bool
Default value: No
Description: Write the simulation time (fs).

TotalEnergy

Type: Bool
Default value: No
Description: Write the total energy value.

Volume

Type: Bool
Default value: No
Description: Write the simulation cell volume, area or length, depending on the system periodicity.

Lattice deformations (volume regimes)¶

The Deformation block can be used to gradually deform the periodic lattice of the system during a MD simulation. This block can be repeated to define multiple deformations, which will be applied on every MD step in the order in which they are listed in the input.

See also

Example demonstrating various lattice deformations
The ReactionsDiscovery workflow uses lattice deformations to predict chemical reactions

Warning

While a Deformation and a Barostat can be used at the same time, remember to set the Scale parameter of the barostat so that no dimension is simultaneously being deformed and barostatted.

Each Deformation block will be active on MD steps between StartStep and StopStep.

The time dependence of the lattice parameters is defined by the Type key:

Linear: This deformation type adds the same constant amount to the selected lattice parameters on every simulation step. When used with TargetLattice, LatticeVelocity, or StrainRate, the lattice matrix \(H\) evolves as \(H(t) = H_0 + \Delta H \cdot t\), where \(H_0\) is the lattice at StartStep.
Exponential: When used with StrainRate, this type strains the lattice by the given strain matrix \epsilon on every step, so that the lattice matrix \(H\) evolves as \(H(t) = H_0 (1 + \epsilon)^t\). When used with LengthRate, the length of each lattice vector evolves as \(l(t) = l_0 (1 + r)^t\).
Sine: This is a periodic deformation going from the starting value of the selected lattice parameters to a set target, and then with the same amplitude to the opposite direction from the starting lattice.
Cosine: This periodic deformation oscillates between the starting lattice and a defined target.

The period of the oscillation for the Sine and Cosine types must be set using the Period key.

The extent of the deformation is defined by setting one of the six mutually exclusive input keys. These belong to two groups, depending on whether they operate on the lattice matrix as a whole, or just on the lengths of the individual lattice vectors:

TargetLattice, Velocity, and Rate: These input keys expect a “lattice-like” matrix of numbers, consisting of up to three rows containing up to three values each. Each row contains the components of a single lattice vector and corresponds to a row of the Lattice block. For systems with 1D or 2D periodicity the matrix may be padded to 3x3 with zeros.
TargetLength, LengthVelocity, and LengthRate: These input keys expect a list of up to three values, defining the desired length of each lattice vector or the (absolute or relative) rate of its change.

MolecularDynamics

Deformation

Type: Block
Recurring: True
Description: Deform the periodic lattice of the system during the simulation.

LatticeVelocity

Type: Non-standard block
Description: Velocity of individual lattice vector components in Angstrom/fs. The format is identical to the System%Lattice block. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).

LengthRate

Type: Float List
Default value: [0.0, 0.0, 0.0]
Description: Relative rate of change of each lattice vector per step.

LengthVelocity

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom/fs
Description: Change the length of each lattice vector with this velocity. With Type=Exponential, LengthVelocity is divided by the current lattice vector lengths on StartStep to determine a LengthRate, which is then applied on all subsequent steps. For Type Sine and Cosine, this defines the maximum velocity (at the inflection point).

Period

Type: Float
Unit: Femtoseconds
Description: Period of oscillation for Type Sine and Cosine.

ScaleAtoms

Type: Bool
Default value: Yes
Description: Scale the atomic positions together with the lattice vectors. Disable this to deform only the lattice, keeping the coordinates of atoms unchanged.

StartStep

Type: Integer
Default value: 1
Description: First step at which the deformation will be applied.

StopStep

Type: Integer
Default value: 0
Description: Last step at which the deformation will be applied. If unset or zero, nSteps will be used instead.

StrainRate

Type: Non-standard block
Description: Strain rate matrix to be applied on every step. The format is identical to the System%Lattice block.

TargetLattice

Type: Non-standard block
Description: Target lattice vectors to be achieved by StopStep. The format is identical to the System%Lattice block.

TargetLength

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom
Description: Target lengths of each lattice vector to be achieved by StopStep. The number of values should equal the periodicity of the system. If a value is zero, the corresponding lattice vector will not be modified.

Type

Type: Multiple Choice
Default value: Linear
Options: [Linear, Exponential, Sine, Cosine]
Description: Function defining the time dependence of the deformed lattice parameters. Linear increments the lattice parameters by the same absolute amount every timestep. Exponential multiplies the lattice parameters by the same factor every timestep. Only StrainRate, LengthRate, and LengthVelocity are supported for Type=Exponential. Sine deforms the system from the starting lattice to TargetLattice/TargetLength and then by the same amount to the opposite direction, while Cosine deforms the system from the starting lattice to the target and back.

Example: Transition from the initial lattice to a 10 Å cube over 1000 steps:

MolecularDynamics
   Deformation
      StopStep 1000
      TargetLattice
         10.0  0.0  0.0
          0.0 10.0  0.0
          0.0  0.0 10.0
      End
   End
End

Example: Oscillate the length of the c lattice vector between the initial value and 20 Å, leaving the a and b vectors unchanged:

MolecularDynamics
   Deformation
      Type Cosine
      Period 100
      TargetLength 0 0 20
   End
End

Example: Stretch the box in the “z” direction by a true exponential strain of 10 ppm per timestep while barostatting the remaining dimensions:

MolecularDynamics
   Barostat Type=MTK Pressure=1e5 Tau=1000 Scale=XY
   Deformation
      Type Exponential
      StrainRate
          0.0  0.0  0.0
          0.0  0.0  0.0
          0.0  0.0 1e-5
      End
   End
End

Molecule Gun: adding molecules during simulation¶

The molecule gun allows you to “shoot” (add with velocity) a molecule into the simulation box.

See also

The GUI tutorial on the molecule gun.

Molecules can be continuously added to the simulation or only once. The initial position can be pre-set or be random within the simulation box or a part thereof. It can be defined either in the Cartesian or fractional coordinates. The initial velocity can be specified either directly (in Angstrom per femtosecond) or as translational temperature or kinetic energy. Possible applications of the molecule gun include e.g. the simulation of enforced collisions or deposition processes on surfaces.

MolecularDynamics

AddMolecules

Type: Block
Recurring: True
GUI name: Add molecules
Description: This block controls adding molecules to the system (a.k.a. the Molecule Gun). Multiple occurrences of this block are possible. By default, molecules are added at random positions in the simulation box with velocity matching the current system temperature. The initial position can be modified using one of the following keywords: Coords, CoordsBox, FractionalCoords, FractionalCoordsBox. The Coords and FractionalCoords keys can optionally be accompanied by CoordsSigma or FractionalCoordsSigma, respectively.

AtomTemperature

Type: Float
Default value: 0.0
Unit: Kelvin
Description: Add random velocity corresponding to the specified temperature to individual atoms of the molecule. This only affects rotational and internal degrees of freedom, not the net translational velocity of the inserted molecule as set by the other options.

ContactDistance

Type: Float
Default value: 0.0
Unit: Angstrom
Description: Translate the bullet along the velocity vector until it comes within ContactDistance of any other atom.

Coords

Type: Float List
Unit: Angstrom
Description: Place molecules at or around the specified Cartesian coordinates. This setting takes precedence over other ways to specify initial coordinates of the molecule: [CoordsBox], [FractionalCoords], and [FractionalCoordsBox].

CoordsBox

Type: Float List
Unit: Angstrom
Description: Place molecules at random locations inside the specified box in Cartesian coordinates. Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. This setting is ignored if Coords is used. In AMSinput, if this field is not empty it will be used instead of the default Coords.

CoordsSigma

Type: Float List
Unit: Angstrom
Description: Sigma values (one per Cartesian axis) for a Gauss distribution of the initial coordinates. Can only be used together with Coords.

DeviationAngle

Type: Float
Default value: 0.0
Unit: Degree
Description: Randomly tilt the shooting direction up to this angle away from the VelocityDirection vector.

Energy

Type: Float
Unit: Hartree
Description: Initial kinetic energy of the molecule in the shooting direction.

EnergySigma

Type: Float
Default value: 0.0
Unit: Hartree
Description: Sigma value for the Gauss distribution of the initial kinetic energy around the specified value. Should only be used together with Energy.

FractionalCoords

Type: Float List
Description: Place molecules at or around the specified fractional coordinates in the main system’s lattice. For non-periodic dimensions a Cartesian value in Angstrom is expected. This setting is ignored if [Coords] or [CoordsBox] is used.

FractionalCoordsBox

Type: Float List
Description: Place molecules at random locations inside the box specified as fractional coordinates in the main system’s lattice. Coordinates of the box corners are specified as: Xmin, Xmax, Ymin, Ymax, Zmin, Zmax. For non-periodic dimensions the Cartesian value in Angstrom is expected. This setting is ignored if [Coords], [CoordsBox], or [FractionalCoords] is used.

FractionalCoordsSigma

Type: Float List
Description: Sigma values (one per axis) for a Gauss distribution of the initial coordinates. For non-periodic dimensions the Cartesian value in Angstrom is expected. Can only be used together with FractionalCoords.

Frequency

Type: Integer
Default value: 0
Description: A molecule is added every [Frequency] steps after the StartStep. There is never a molecule added at step 0.

MinDistance

Type: Float
Default value: 0.0
Unit: Angstrom
Description: Keep the minimal distance to other atoms of the system when adding the molecule.

MoleFraction

Type: Float
Description: Defines a mixture to be deposited using one AddMolecules block per component. AMS will randomly alternate between any guns that have MoleFraction set. These need to all have the same settings for StartStep, StopStep and Frequency. Any additional AddMolecules blocks without MoleFraction will remain completely independent.

NumAttempts

Type: Integer
Default value: 10
Description: Try adding the molecule up to the specified number of times or until the MinDistance constraint is satisfied. If all attempts fail a message will be printed and the simulation will continue normally.

Rotate

Type: Bool
Default value: No
Description: Rotate the molecule randomly before adding it to the system.

StartStep

Type: Integer
Default value: 0
Description: Step number when the first molecule should be added. After that, molecules are added every Frequency steps. For example, ff StartStep=99 and Frequency=100 then a molecule will be added at steps 99, 199, 299, etc… No molecule will be added at step 0, so if StartStep=0 the first molecule is added at the step number equal to [Frequency].

StopStep

Type: Integer
Description: Do not add this molecule after the specified step.

System

Type: String
Description: String ID of the [System] that will be added with this ‘gun’. The lattice specified with this System is ignored and the main system’s lattice is used instead. AMSinput adds the system at the coordinates of the System (thus setting Coords to the center of the System).

Temperature

Type: Float
Unit: Kelvin
Description: Initial energy of the molecule in the shooting direction will correspond to the given temperature.

TemperatureSigma

Type: Float
Default value: 0.0
Unit: Kelvin
Description: Sigma value for the Gauss distribution of the initial temperature the specified value. Should only be used together with Temperature.

Velocity

Type: Float
Unit: Angstrom/fs
Description: Initial velocity of the molecule in the shooting direction.

VelocityDirection

Type: Float List
Description: Velocity direction vector for aimed shooting. It will be random if not specified. In AMSinput add one or two atoms (which may be dummies). One atom: use vector from center of the system to add to that atom. Two atoms: use vector from the first to the second atom.

VelocitySigma

Type: Float
Default value: 0.0
Unit: Angstrom/fs
Description: Sigma value for the Gauss distribution of the initial velocity around the specified value. Should only be used together with Velocity.

Since the 2022 release of the AMS driver, it is possible to generate molecule mixtures by using multiple guns that each have the MoleFraction keyword set: AMS will then randomly alternate between any of these guns. The cooperating guns need to all have the same settings for StartStep, StopStep and Frequency. (Any additional AddMolecules blocks without MoleFraction will remain completely independent.) The following example shows the generation of a 80:20 mixture of molA and molB:

MolecularDynamics
   AddMolecules
       System molA
       MoleFraction 0.8
       Frequency 2000
       StartStep 1
   End
   AddMolecules
       System molB
       MoleFraction 0.2
       Frequency 2000
       StartStep 1
   End
End

System anthracene
   ...
End

System benzene
   ...
End

Note that the exact number of inserted molecules of each type is not deterministic: running the same job twice may give you slightly different ratios. However, when running the job many times, the relative ratios averaged over the different runs should approach the fractions as requested in the input.

Removing molecules during simulation¶

Molecules detected by the AMS driver can also be removed from the system. This feature can, for example, be used to remove reaction products.

MolecularDynamics

RemoveMolecules

Type: Block
Recurring: True
GUI name: Remove molecules
Description: This block controls removal of molecules from the system. Multiple occurrences of this block are possible.

Formula

Type: String
Description: Molecular formula of the molecules that should be removed from the system. The order of elements in the formula is very important and the correct order is: C, H, all other elements in the strictly alphabetic order. Element names are case-sensitive, spaces in the formula are not allowed. Digit ‘1’ must be omitted. Valid formula examples: C2H6O, H2O, O2S. Invalid formula examples: C2H5OH, H2O1, OH, SO2. Invalid formulas are silently ignored. Use * to remove any molecule, which must be combined with SinkBox or SafeBox.

Frequency

Type: Integer
Default value: 0
Description: The specified molecules are removed every so many steps after the StartStep. There is never a molecule removed at step 0.

SafeBox

Type: Block
Description: Part of the simulation box where molecules may not be removed. Only one of the SinkBox or SafeBox blocks may be present. If this block is present the molecule will not be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.

Amax

Type: Float
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Description: Coordinate of the lower bound along the third axis.

FractionalCoordsBox

Type: Float List
GUI name: Safe box
Description: Do not remove molecules that are (partly) inside the safe box. Borders of the safe box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax. For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.

SinkBox

Type: Block
Description: Part of the simulation box where matching molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present then such a molecule will only be removed if any of its atoms is within the box. For a periodic dimension it is given as a fraction of the simulation box (the full 0 to 1 range by default). For a non-periodic dimension it represents absolute Cartesian coordinates in Angstrom.

Amax

Type: Float
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Description: Coordinate of the lower bound along the third axis.

FractionalCoordsBox

Type: Float List
GUI name: Sink box
Description: Remove molecules that are (partly) inside the sink box. Borders of the sink box specified as: Amin, Amax, Bmin, Bmax, Cmin, Cmax. For periodic dimensions fractional coordinates between 0 and 1 and for non-periodic dimensions Cartesian values in Angstrom are expected.

StartStep

Type: Integer
Default value: 0
Description: Step number when molecules are removed for the first time. After that, molecules are removed every [Frequency] steps. For example, if StartStep=99 and Frequency=100 then molecules will be removed at steps 99, 199, 299, etc… No molecule will be removed at step 0, so if StartStep=0 the first molecules are removed at the step number equal to [Frequency].

StopStep

Type: Integer
Description: Do not remove the specified molecules after this step.

Warning

When there is a Molecules%AdsorptionSupportRegion defined, the molecule formulas depend on whether the molecule is adsorbed or not.

Accelerated dynamics¶

The PLUMED library support in AMS¶

PLUMED is a plugin that works with various MD programs and is also available in AMS. It can be used for on-the-fly analysis of the dynamics, or to perform a wide variety of free energy methods. The interface with the plugin is really simple: you just need to specify the PLUMED input in the MolecularDynamics%Plumed%Input block and it will be passed to the library “as is”. At each MD step, the current state of the system will be passed to the plugin to be updated according to the PLUMED input.

MolecularDynamics

Plumed

Type: Block
Description: Input for PLUMED. The parallel option is still experimental.

Input

Type: Non-standard block
Description: Input for PLUMED. Contents of this block is passed to PLUMED as is.

Parallel

Type: Block
Description: Options for double parallelization, which allows to split the available processor cores into groups working through all the available tasks in parallel, resulting in a better parallel performance. The keys in this block determine how to split the available processor cores into groups working in parallel.

nCoresPerGroup

Type: Integer
GUI name: Cores per group
Description: Number of cores in each working group.

nGroups

Type: Integer
GUI name: Number of groups
Description: Total number of processor groups. This is the number of tasks that will be executed in parallel.

nNodesPerGroup

Type: Integer
GUI name: Nodes per group
Description: Number of nodes in each group. This option should only be used on homogeneous compute clusters, where all used compute nodes have the same number of processor cores.

Metadynamics for Conformer-Rotamer Ensemble Sampling (CREST-MTD)¶

This is a very specific implementation of metadynamics that is only meant for exploration of conformer space, as used in the Conformer-Rotamer Ensemble Sampling (CREST) approach. It is an RMSD-based metadynamics that places a new 1-dimensional Gaussian on the potential energy surface every NSteps steps. The Gaussian is a function of the RMSD from the current geometry, which will always be zero at the moment of placement. All Gaussians have the same maximum height (Height) and the same width (Width). There is an upper limit of NGaussiansMax to the number of Gaussians present in the system, and when this is exceeded the oldest Gaussian is removed. By default the Gaussians are gradually introduced, using a scaling function that increases exponentially from 0 to 1 with the simulation time. The keyword ScalingSlope in the input block GaussianScaling determines the slope of the scaling function with respect to time. The default value of 0.03 \(steps^{-1}\) yields a scaling factor of nearly 1 after 100 steps. The keyword ScaleGaussians in the inputblock GaussianScaling determines whether the Gaussians are scaled at all.

By default, all atoms are included in the RMSD calculation. However, the selection can be restricted to specific regions using the Region keyword. This can be a single region or a combination thereof using region expressions (for example, reg1+reg2 for a union).

MolecularDynamics

CRESTMTD

Type: Block
GUI name: CREST_MTD
Description: Input for CREST metadynamics simulation.

AddEnergy

Type: Bool
Default value: No
Description: Add the bias energy to the potential energy (to match the gradients)

GaussianScaling

Type: Block
Description: Options for gradual introduction of the Gaussians

ScaleGaussians

Type: Bool
Default value: Yes
Description: Introduce the Gaussians gradually, using a scaling function

ScalingSlope

Type: Float
Default value: 0.03
Description: Slope of the scaling function for the Gaussians with respect to time

Height

Type: Float
Unit: Hartree
Description: The height of the Gaussians added

NGaussiansMax

Type: Integer
Description: Maximum number of Gaussians stored

NSteps

Type: Integer
Description: Interval of Gaussian placement

Region

Type: String
Default value: *
Description: Restrict the range of atoms for RMSD calculation to the specified region.

RestartFile

Type: String
Description: Filename for file from which to read data on Gaussians placed previously.

Width

Type: Float
Unit: Bohr
Description: The width of the Gaussians added in terms of the RMSD

By default, the gradients of the Gaussians with respect to the atom coordinates are added to the state gradients, but the value of the Gaussians is not added to the energy, which is common in metadynamics. For testing purposes it can be useful to add the Gaussian value to the energy, and this can be done with the keyword AddEnergy. Irrespective of this choice, the energy value of the Gaussian at each geometry is printed in the ams.rkf file in the section CrestMTDHistory. It is also possible to use Gaussians from an earlier CREST-MTD simulation, using the keyword RestartFile.

Collective Variable-driven HyperDynamics (CVHD)¶

The Collective Variable-driven HyperDynamics is a molecular dynamics acceleration method that allows observation of rare events by filling energy minima with a bias potential. In this sense it is similar to metadynamics. The difference of the hyperdynamics is that it ensures that the bias disappears in the transition state region. This difference allows hyperdynamics to calculate the rate of slow processes, for example the ignition phase of combustion.

See also

The GUI tutorial on CVHD.

The CVHD implementation in AMS follows the algorithm described in K.M. Bal, E.C. Neyts, JCTC, 11 (2015)

The StartStep, Frequency, StopStep, and WaitSteps keys define when and how often the bias potential is added, and when it is removed. The Bias block defines parameters of the bias potential peaks and the ColVarBB block describes parameters of the bond-breaking collective variable.

MolecularDynamics

CVHD

Type: Block
Recurring: True
GUI name: CVHD
Description: Input for the Collective Variable-driven HyperDynamics (CVHD).

Bias

Type: Block
Description: The bias is built from a series of Gaussian peaks deposited on the collective variable axis every [Frequency] steps during MD. Each peak is characterized by its (possibly damped) height and the RMS width (standard deviation).

DampingTemp

Type: Float
Default value: 0.0
Unit: Kelvin
GUI name: Bias damping T
Description: During well-tempered hyperdynamics the height of the added bias is scaled down with an exp(-E/kT) factor [PhysRevLett 100, 020603 (2008)], where E is the current value of the bias at the given CV value and T is the damping temperature DampingTemp. If DampingTemp is zero then no damping is applied.

Delta

Type: Float
Description: Standard deviation parameter of the Gaussian bias peak.

Height

Type: Float
Unit: Hartree
Description: Height of the Gaussian bias peak.

ColVarBB

Type: Block
Recurring: True
GUI name: Collective Variable
Description: Description of a bond-breaking collective variable (CV) as described in [Bal & Neyts, JCTC, 11 (2015)]. A collective variable may consist of multiple ColVar blocks.

at1

Type: Block
Description: Specifies the first bonded atom in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: Atom type name of the first atom of the bond. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.

at2

Type: Block
Description: Specifies the second bonded atom in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection of bonded atoms to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: Atom type name of the second atom of the bond. The value is allowed to be the same as [at1], in which case bonds between atoms of the same type will be included.

cutoff

Type: Float
Default value: 0.3
GUI name: Bond order cutoff
Description: Bond order cutoff. Bonds with BO below this value are ignored when creating the initial bond list for the CV. The bond list does not change during lifetime of the variable even if some bond orders drop below the cutoff.

p

Type: Integer
Default value: 6
GUI name: Exponent p
Description: Exponent value p used to calculate the p-norm for this CV.

rmax

Type: Float
Unit: Angstrom
GUI name: R max
Description: Max bond distance parameter Rmax used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.

rmin

Type: Float
Unit: Angstrom
GUI name: R min
Description: Min bond distance parameter Rmin used for calculating the CV. It should be close to equilibrium distance for the corresponding bond.

ColVarBM

Type: Block
Recurring: True
GUI name: Collective Variable
Description: Description of a bond-making collective variable (CV). A collective variable may consist of multiple ColVar blocks.

at1

Type: Block
Description: Specifies selection criteria for the first atom of a pair in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: Atom type name of the first atom of the pair. The name must be as it appears in the System block. That is, if the atom name contains an extension (e.g C.1) then the full name including the extension must be used here.

at2

Type: Block
Description: Specifies selection criteria for the second atom of a pair in the collective variable.

region

Type: String
Default value: *
Description: Restrict the selection to a specific region. If this is not set, atoms anywhere in the system will be selected.

symbol

Type: String
Description: Atom type name of the second atom of the pair. The value is allowed to be the same as [at1], in which case pairs of atoms of the same type will be included.

cutoff

Type: Float
Default value: 0.3
GUI name: Bond order cutoff
Description: Bond order cutoff. Bonds with BO above this value are ignored when creating the initial atom-pair list for the CV. The list does not change during lifetime of the variable even if some bond orders rise above the cutoff.

p

Type: Integer
Default value: 6
GUI name: Exponent p
Description: Exponent value p used to calculate the p-norm for this CV.

rmax

Type: Float
Unit: Angstrom
GUI name: R max
Description: Max bond distance parameter Rmax used for calculating the CV. It should be much larger than the corresponding Rmin.

rmin

Type: Float
Unit: Angstrom
GUI name: R min
Description: Min bond distance parameter Rmin used for calculating the CV. It should be close to the transition-state distance for the corresponding bond.

Frequency

Type: Integer
Description: Frequency of adding a new bias peak, in steps. New bias is deposited every [Frequency] steps after [StartStep] if the following conditions are satisfied: the current CV value is less than 0.9 (to avoid creating barriers at the transition state), the step number is greater than or equal to [StartStep], and the step number is less than or equal to [StopStep].

MaxEvents

Type: Integer
Default value: 0
Description: Max number of events to allow during dynamics. When this number is reached no new bias will be added for this input block.

StartStep

Type: Integer
Description: If this key is specified, the first bias will be deposited at this step. Otherwise, the first bias peak is added at the step number equal to the Frequency parameter. The bias is never deposited at step 0.

StopStep

Type: Integer
Description: No bias will be deposited after the specified step. The already deposited bias will continue to be applied until the reaction event occurs. After that no new CVHD will be started. By default, the CVHD runs for the whole duration of the MD calculation.

WaitSteps

Type: Integer
Description: If the CV value becomes equal to 1 and remains at this value for this many steps then the reaction event is considered having taken place. After this, the collective variable will be reset and the bias will be removed.

During a CVHD calculation, the following variables are saved to the MDHistory section of the RKF file, in addition to other MD properties:

BiasEnergy - value the bias energy at the current MD step, in Hartree.
MaxBiasEnergy - max BiasEnergy since the last sampling step.
BoostFactor - the boost factor at the given MD step. The boost factor is calculated at each MD step as \(boost = e^{E_{bias}/kT}\), where T is the MD ensemble temperature.
MaxBoostFactor - max BoostFactor value since the last sampling step.
HyperTime - boosted MD time, in femtoseconds, which is a sum of the hyper-time steps calculated from the current boost factor and the MD time step as \(\Delta t_{boost} = boost * \Delta t\). In hyperdynamics, the hyper-time value is directly related to the rate of the process boosted by the corresponding collective variable.

Temperature Replica Exchange¶

Sampling of rare events can be accelerated using the Replica Exchange Molecular Dynamics (REMD) method, also known as Parallel Tempering. This method runs multiple replicas (copies) of the simulated system in parallel, each in a different ensemble. In the case of Temperature REMD, these ensembles are all NVT or NpT, each at a different temperature. Periodically, Monte Carlo swaps are attempted between neighboring ensembles. If the current configuration of replica A has a sufficient Boltzmann probability in the ensemble of replica B (and vice versa), the two configurations will be swapped. This causes high-energy configuration to migrate into the high-temperature replicas while low-energy configurations eventually end up in the coldest ensemble. This facilitates the crossing of energy barriers in the high-temperature ensembles while keeping the coldest replica at a given temperature of interest. Because each replica always samples an unbiased ensemble, any property can be calculated using standard MD analysis methods without special preparation.

The method is controlled using the ReplicaExchange block:

MolecularDynamics

ReplicaExchange

Type: Block
Description: This block is used for (temperature) Replica Exchange MD (Parallel Tempering) simulations.

AllowWrongResults

Type: Bool
Default value: No
Description: Allow combining Replica Exchange with other features when the combination is known to produce physically incorrect results.

EWMALength

Type: Integer
Default value: 10
Description: Length of the exponentially weighted moving average used to smooth swap probabilities for monitoring. This value is equal to the inverse of the EWMA mixing factor.

SwapFrequency

Type: Integer
Default value: 100
Description: Attempt an exchange every N steps.

TemperatureFactors

Type: Float List
Description: This is the ratio of the temperatures of two successive replicas. The first value sets the temperature of the second replica with respect to the first replica, the second value sets the temperature of the third replica with respect to the second one, and so on. If there are fewer values than nReplicas, the last value of TemperatureFactor is used for all the remaining replicas.

Temperatures

Type: Float List
Description: List of temperatures for all replicas except for the first one. This is mutually exclusive with TemperatureFactors. Exactly nReplicas-1 temperature values need to be specified, in increasing order. The temperature of the first replica is given by [Thermostat%Temperature].

nReplicas

Type: Integer
Default value: 1
GUI name: Number of replicas
Description: Number of replicas to run in parallel.

The number of replicas set by nReplicas must never exceed the total number of processors used for the simulation. If possible, the total number of processors should be an integer multiple of nReplicas to ensure good load balancing.

The temperature of the base (coldest) replica is determined by the Thermostat input block, just like in an ordinary MD simulation. There are two ways to set the temperatures of the remaining replicas, either using Temperatures or TemperatureFactors. The latter is typically more convenient, as it makes it easy to set up the optimal geometric progression of temperatures. In the simplest case, it is enough to supply just a single value in TemperatureFactors, setting the common ratio of temperatures of any two adjacent replicas.

SwapFrequency should be set as low as practical for maximum efficiency. The value of this parameter isn’t critical because it doesn’t affect the validity of the results. However, setting it too high will decrease overall acceleration by missing some opportunities to exchange. Conversely, using a value that is too low will increase the communication overhead and lead to useless back-and-forth swaps between adjacent replicas. Ideally, SwapFrequency should be comparable to the correlation time of the system to ensure that individual exchange attempts are uncorrelated.

The trajectory of each replica is written to a separate RKF file: ams.rkf for the base replica and replicaX.rkf for the other replicas. One can easily switch between these files in the GUI using File → Related Files. In addition to data present in any MD trajectory, these files also contain an extra section ReplicaExchangeHistory with the following data items written every SwapFrequency steps:

AvgSwapProbability – Average swap acceptance for each pair of replicas, smoothed using an exponentially weighted moving average with a mixing factor equal to the inverse of EWMALength.
{Min,Max,Mean,StdDev}PotentialEnergy – Statistics of the potential energy for each ensemble over the last SwapFrequency steps.
SystemInEnsemble i – Identifies the system (continuous trajectory) currently running in ensemble (replica) i.
EnsembleOfSystem i – Inverse mapping of SystemInEnsemble, giving the current replica number in which the system number i runs.
TemperatureOfSystem i – Equivalent to EnsembleOfSystem using temperatures instead of integer numbers to identify ensembles.

These data items can be plotted using the MD Replica Exchange menu in AMSmovie. For example, plotting TemperatureOfSystem or EnsembleOfSystem is useful to visualize the migration of each system through the space of ensembles, where each curve represents one continuous trajectory. Plotting potential energy statistics or average acceptances facilitates tuning the number of replicas and their temperatures to achieve efficient acceleration. The replica exchange method can only work when the potential energy distributions of adjacent ensembles have a sufficient overlap. This can be easily seen by comparing MaxPotentialEnergy of ensemble i with MinPotentialEnergy of ensemble i+1. The optimal degree of overlap is such that leads to approximately 20 % of swap attempts getting accepted. The acceptance of swaps can be monitored by plotting AvgSwapProbability and the corresponding TemperatureFactors can then be adjusted to keep it near the optimal value.

Bond Boost Method¶

The bond boost method implemented here is described in 3. In this method, the distances between atoms that are relevant to the reaction of interest are calculated to determine the orientation of the reactant molecules. If a suitable initial configuration is recognized, an additional restraint energy (possibly consisting of more than one term) is added to the system that is intended to stretch or compress bonds at a pre-defined rate such that this additional energy can help achieve the energy to cross the reaction barrier. A single term of the restraint energy is depends on the restraints type and its parameters, see restraint definitions for details. If more than one suitable configuration is found then the one with the smallest sum of distances is used to create the restraints.

See also

The GUI tutorial on the Bond Boost Method.

MolecularDynamics

BondBoost

Type: Block
Recurring: True
Description: Forced reaction (bond boost) definitions. Multiple BondBoost blocks may be specified, which will be treated independently.

Chain

Type: Block
Description: Specifications of a chain of atoms. When a chain is detected the distance restraints will be activated. No other chain of this type will be detected while any restraints for this chain is active.

AtomNames

Type: String
Description: Atom names specifying the chain. An atom name can optionally be followed by ‘@’ and a region name, in this case only atoms of this type from the given region will be matched. A leading ‘@’ followed by a number indicates that this position in the chain must be occupied by the atom found earlier at the specified position in the chain. For example “O H N C @1” indicates that the last atom in the chain of the five atoms must be the first oxygen, thus defining a 4-membered ring. This is the only way to define a ring because implicit rings will not be detected. For example, “O H N C O” does not include rings.

MaxDistances

Type: Float List
Unit: Angstrom
Description: Maximum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.

MinDistances

Type: Float List
Unit: Angstrom
Description: Minimum distances for each pair of atoms in the chain. The number of distances must be one less than the number of AtomNames.

DistanceRestraint

Type: String
Recurring: True
Description: Specify two atom indices followed by the optimum distance in Angstrom, the first parameter and, optionally, the profile type and the second parameter. This restraint will try to keep the distance between the two specified atoms at the given value. For periodic systems this restraint follows the minimum image convention. Each atom index indicates a position of the corresponding atom in the AtomNames key. Currently recognized restraint profile types: Harmonic (default), Hyperbolic, Erf, GaussianWell. The first parameter is the force constant for the Harmonic, Hyperbolic, and Erf profiles, or well depth for GaussianWell. The second parameter is the asymptotic force value F(Inf) for Hyperbolic and Erf profiles, or the factor before x^2 in the exponent for GaussianWell. Note: the GaussianWell restraint should be used with the Moving flag.

Moving

Type: Bool
Default value: No
GUI name: Move restraint
Description: Move the restraints created with this BondBoost. The restraint value will start at the current coordinate’s value and will move towards the optimum during the restraint’s lifetime. The increment is calculated from the initial deviation and the [NSteps] parameter. This feature should be used with the GaussianWell restraint types.

NSteps

Type: Integer
GUI name: Boost lifetime
Description: Number of steps the restraints will remain active until removed. Atoms participating in one reaction are not available for the given number of steps.

NumInstances

Type: Integer
Default value: 1
GUI name: Number of instances
Description: Number of reactions of this type taking place simultaneously.

Units

Type: Multiple Choice
Default value: Default
Options: [Default, MD]
GUI name: Restr. parameter units
Description: Change energy, force and force constant units in the DistanceRestraint key from the default (atomic units) to those often used in the MD community (based on kcal/mol and Angstrom). Units for the optimum distances are not affected.

For example:

MolecularDynamics
   BondBoost
      NSteps 10000
      Chain
         AtomNames     N.1   C.t    O     H     @1
         MinDistances     3.0   1.2   1.5   0.8
         MaxDistances     3.8   3.0   2.5   1.5
      End
#     Restraints         i  j   R_0    FC
      DistanceRestraint  1  2   1.5   0.05   Hyperbolic   0.7
      DistanceRestraint  2  3   3.5   0.03   Hyperbolic   0.5
      DistanceRestraint  3  4   1.0   0.03   Hyperbolic   0.5
   End
End

The AtomNames, MinDistances, and MaxDistances keys constitute the atom chain definitions for the initial configuration. Thus, the example above defines a chain of atoms N.1-C.t-O-H-N.1 with R(N.1-C) in the (3.0,3.8) range, R(C.t-O) in the (1.2,3.0) range, etc.. In this example, the last atoms in the chain is required to be the same as the fist one, thus defining a ring. The specified restraints will push pairs of atoms C-N and O-H close together, which will hopefully let them form a bond, and pull atoms C.t and O away from each other, thus breaking the C-O bond. The restraint type is set to Hyperbolic to avoid very large forces that would otherwise result from a harmonic potential at a large deviation.

Note

When detecting coordinates, the program uses the full atom name and not just the element name. An atom name consists of the element name optionally followed by a period and a suffix, just like N.1 and C.t in the example above. Using extended names for some atoms one may allow only a subset of bonds to be boosted.

Reaction boost (Targeted MD)¶

The principle of targeted (or steered) MD is simple: during molecular dynamics, the system is pushed towards a certain known configuration in small steps. The steering can be in the form of holonomic constraints, then it is the standard Targeted MD (TMD). When restraints instead of constraints are used, then some authors call it steered MD 6.

The ReactionBoost feature uses restraints to push the system towards the target configuration. The restraints can be one of the following two types: atom-pair or (mass-weighted) RMSD. In both cases, the user can select a region to which the steering will be limited. AMS will then apply the restraints only to the atoms of the region(s). The RMSD type of restraints is suitable for very large systems or regions while the pair restraints can be used for small to moderately-sized ones. The atom-pair restraints can be further sub-divided into the following types, depending on the mutual bonding situation of the two atoms in the initial and the final state: bonded, non-bonded, bond-breaking and bond-making. The type is determined automatically at the time the steering is started based on the interatomic distances and the covalent radii of the atoms. A non-bonded restraint is a static repulsive potential, it is intended to keep atoms from forming a bond. The other three are moving: the restraint’s target distance changes between its initial and final values as the MD progresses. Setting the profile to None disables the corresponding pair restraint type.

The following keys define parameters of the method:

MolecularDynamics

ReactionBoost

Type: Block
GUI name: Reaction Boost
Description: Define a series of transitions between different states of the system. Each transition is defined by a TargetSystem and by a set of restraints that force the transition.

BondBreakingRestraints

Type: Block
Description: Define parameters for moving restraints that are added for pairs of atoms that become disconnected during the transition. It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.

Erf

Type: Block
Description: Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

Taper

Type: Block
Description

Enabled

Type: Bool
Default value: No
GUI name: Tapering
Description: Enable tapering of the restraint potential and force between the given range of bond distances. A 7-th order tapering function on the actual (not target!) distance will be used. The MaxDistance must be greater than MinDistance.

MaxDistance

Type: Float
Default value: 0.0
Unit: Angstrom
GUI name: End tapering at
Description: Bond length at which the restraint potential and force decays to zero.

MinDistance

Type: Float
Default value: 0.0
Unit: Angstrom
GUI name: Start tapering at
Description: Bond length at which the restraint potential and force will start decaying to zero.

Type

Type: Multiple Choice
Default value: Erf
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Bond breaking restraints
Description: Select type of the moving restraint profile. Harmonic: V=0.5*FC*(r-r0)^2 Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1) Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)) GaussianWell: V=WellDepth*(1-exp(-Sigma*(r-r0)^2)) Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta. The force for Hyperbolic and Erf is bounded by a user-defined value, the latter converging to it faster than the former. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable. Moving restraints are added for pairs of atoms that become disconnected during the transition. It is intended to make sure the corresponding bonds get broken, although this may not always be required because forming other bonds will likely get these bonds broken.

BondMakingRestraints

Type: Block
Description: Define parameters for moving restraints that are added for pairs of atoms that become connected during the transition. It is intended to make sure the bonds are created as required.

Erf

Type: Block
Description: Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

Type

Type: Multiple Choice
Default value: Erf
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Bond making restraints
Description: Select type of the moving restraint profile. Harmonic: V=0.5*FC*(r-r0)^2 Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1) Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)) GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2) Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta. The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable. Moving restraints are added for pairs of atoms that become connected during the transition. It is intended to make sure the bonds are created as required.

BondedRestraints

Type: Block
Description: Define parameters for bonded restraints. A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state. It is intended to make sure they remain bonded during simulation.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Type

Type: Multiple Choice
Default value: None
Options: [None, Harmonic]
GUI name: Bonded restraints
Description: Select type of the bonded restraints: Harmonic: V=0.5*FC*(r-r0)^2 A bonded restraint is added for each pair of atoms that are bonded both in the current and in the final state. It is intended to make sure they remain bonded during simulation.

Change

Type: Multiple Choice
Default value: TargetCoordinate
Options: [TargetCoordinate, Force, LogForce]
GUI name: Move type
Description: Select what to change during dynamics. By default, once the restraints are switched on, AMS will change the restraint’s target coordinate towards its final value. If the [Force] or [LogForce] option is selected then the target coordinate is set to its final value immediately and instead the restraint force is gradually scaled from 0 to 1. The scaling is either linear (Force) or logarithmic (LogForce).

InitialFraction

Type: Float
Default value: 0.0
Description: Initial fraction of the boost variable. At the first boosting step, the restraint’s target value (or force or log(force)) is equal to InitialFraction + 1/NSteps.

InterEquilibrationSteps

Type: Integer
Default value: 0
Description: Number of equilibration steps after reaching a target before setting up restraints for the next one.

MinBondChange

Type: Float
Default value: 1.0
Unit: Bohr
Description: Minimal change in the distance for an individual restraint to be considered bond-breaking/making vs bonded.

MinBondStrength

Type: Float
Default value: 0.5
Description: Minimum strength (usually ranges from 0 to 1) for a bond to be considered.

NSteps

Type: Integer
Default value: 500
GUI name: Steps per target
Description: Number of steps per target the restraints should be active for.

NonBondedRestraints

Type: Block
Description: Define parameters for non-bonded restraints. A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state. It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential

Exponential

Type: Block
Description: Define parameters for the repulsive potential V=Epsilon*exp(-Sigma*r).

Epsilon

Type: Float
Default value: 1.0
Unit: Hartree
Description: Epsilon parameter in the repulsive potential expression.

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr
Description: Sigma parameter in the repulsive potential expression.

Type

Type: Multiple Choice
Default value: None
Options: [None, Exponential]
GUI name: Non-bonded restraints
Description: Select type of the non-bonded restraints: Exponential: V=Epsilon*exp(-Sigma*r) A non-bonded restraint is added for each pair of atoms that are bonded neither in the current nor in the final state. It is intended to keep them from forming a bond unintentionally. They are represented by a repulsive potential.

PreEquilibrationSteps

Type: Integer
Default value: 0
Description: Number of steps before enabling the first set of restraints.

RMSDRestraint

Type: Block
GUI name: RMSD restraint
Description: Define a static restraint that pulls each atom to its position in the target system, but in contrast to the individual restraints, the force for this one depends on the total mass-weighted root-mean-squared distance (RMSD) between the two structures.

Erf

Type: Block
Description: Define parameters for the Int(erf) potential V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI)). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

GaussianWell

Type: Block
Description: Define parameters in the Gaussian well potential V=-WellDepth*exp(-Sigma*(r-r0)^2).

Sigma

Type: Float
Default value: 1.0
Unit: 1/Bohr^2
Description: Sigma parameter in the potential expression.

WellDepth

Type: Float
Default value: 1.0
Unit: Hartree
Description: WellDepth parameter in the potential expression.

Harmonic

Type: Block
Description: Define parameters for the harmonic potential V=0.5*FC*(r-r0)^2.

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The FC parameter of the harmonic potential.

Hyperbolic

Type: Block
Description: Define parameters for the hyperbolic potential V=alpha*(sqrt(1 + beta*x^2) - 1). The alpha and beta parameters are computed from the user-defined ForceConstant and MaxForce: beta=ForceConstant/MaxForce, alpha=MaxForce/beta

ForceConstant

Type: Float
Default value: 0.5
Unit: Hartree/Bohr^2
Description: The force constant (second derivative of the potential) at the optimum point.

MaxForce

Type: Float
Default value: 0.05
Unit: Hartree/Bohr
Description: Asymptotic value of the force at the infinity.

Type

Type: Multiple Choice
Default value: None
Options: [None, Harmonic, Hyperbolic, Erf, GaussianWell]
GUI name: Type
Description: Select type of the RMSD restraint profile: Harmonic: V=0.5*FC*(r-r0)^2 Hyperbolic: V=alpha*(sqrt(1 + beta*x^2) - 1) Erf: V = alpha*(beta*x*erf(beta*x) + (exp(-(beta*x)**2) - 1)/sqrt(PI), GaussianWell: V=-WellDepth*exp(-Sigma*(r-r0)^2) Here beta=ForceConstant/MaxForce, alpha=MaxForce/beta. The Harmonic profile can be problematic at large deviations as it may result in large forces. The force for Hyperbolic and Erf is bounded by a user-defined value. The GaussianWell has a finite depth so it is suitable for cases when crossing a high reaction barrier is not desirable.

Region

Type: String
Default value: *
GUI name: Region
Description: Region to which the restraints should be limited.

TargetSystem

Type: String
Recurring: True
GUI name: Target system
Description: The target system’s name for this transition. Multiple targets can be specified to request multiple transitions in one simulation. Note that only the lattice and the atomic coordinates of the target system are used and other properties (bonds, charge, etc.) are ignored. The target system’s lattice is used only to determine connections and it cannot be restrained.

Type

Type: Multiple Choice
Default value: None
Options: [None, Pair, RMSD]
GUI name: Restraint set type
Description: Reaction Boost uses a series of transitions between different states of the system. Each transition is defined by a TargetSystem and by a set of restraints that force the transition. Select the type of the restraint set: -None: no Reaction Boost - Pair: use pair restraints - RMSD: use RMSD restraints. Pair restraints are defined per atom pair while the RMSD defines one collective restraint for all atoms and is thus suitable for very large systems. The pair restraints are further divided into four sub-types: bonding, non-bonding, bond-breaking and bond-making. The sub-type of restraints for each pair is determined automatically depending on whether the two atoms are bonded in the initial/final state. Parameters of the pair restraints are defined by [NonBondedRestraints], [BondedRestraints], [BondBreakingRestraints] and [BondMakingRestraints] blocks, while those of the RMSD restraint by the [RMSDRestraint] block.

Force bias Monte Carlo (fbMC)¶

Configurational sampling and structural relaxation can be accelerated by the Force bias Monte Carlo method. Unlike molecular dynamics, this approach does not use the equations of motion or atomic velocities. Instead, all atoms are randomly displaced in each fbMC steps. AMS uses an uniform-acceptance force bias Monte Carlo flavour of fbMC called tfMC, as published by Mees et al. 4 Unlike other well-known Monte Carlo methods such as the Metropolis algorithm, fbMC does not generate completely random moves and then test whether these should be accepted or rejected. Instead, the atomic displacements are generated so that atoms preferably move in the direction of the forces acting on them. This special biasing enables fbMC to accept every move, sampling the correct canonical ensemble with high efficiency.

In AMS the fbMC method is implemented as an add-on to molecular dynamics, enabling mixed MC-MD simulations. After every Frequency MD steps, the MD procedure is stopped and fbMC takes over, executing NSteps Monte Carlo steps. Once the fbMC procedure completes, the MD simulation continues from the new geometry generated by fbMC while reusing atomic velocities from before the start of fbMC.

The fbMC module requires three main input settings. Apart from the NSteps and Frequency defining the mix of molecular dynamics and Monte Carlo, Temperature needs to be set as desired to sample a particular canonical (NVT) ensemble. Although the fbMC procedure always runs in constant temperature mode, the rest of the MD simulation can in principle use any ensemble (with or without a thermostat or barostat).

Note

To run a pure fbMC simulation with no molecular dynamics component, leave Frequency set to 1 (the default), set the MD TimeStep and InitialVelocities to zero, and do not use other MD features such as a thermostat or a barostat.

Note

AMS currently cannot write sampled geometries to the trajectory during the fbMC procedure. To see the evolution of the system during a long fbMC run, split it into multiple shorter fbMC passes to let the MD driver sample the current state between them. To do this, set the NSteps for fbMC to the desired trajectory sampling interval, keep Frequency set to 1 and set Trajectory SamplingFreq to 1.

The amount of acceleration provided by fbMC depends on the StepLength parameter, which defines the maximum displacement of the lightest atom in the system. The default value of 0.1 Å is relatively conservative. Increasing StepLength leads to faster evolution of the system, but setting it too high can lead to inaccurate sampling or cause crashes by generating geometries that are too distorted.

An estimate of the timescale associated with fbMC (tfMC) steps will be printed to the output.

MolecularDynamics

fbMC

Type: Block
Recurring: True
GUI name: fbMC
Description: This block sets up force bias Monte Carlo interleaved with the molecular dynamics simulation.

Frequency

Type: Integer
Default value: 1
Description: Run the fbMC procedure every Frequency MD steps.

MassRoot

Type: Float
Default value: 2.0
Description: Inverse of the exponent used to mass-weight fbMC steps.

MolecularMoves

Type: Block
Description: Move molecules as rigid bodies in addition to normal atomic moves.

Enabled

Type: Bool
Default value: No
GUI name: Enable molecular moves
Description: Enable moving molecules as rigid bodies based on net forces and torques. Ordinary per-atom displacements will then be based on residual atomic forces.

RotationStepAngle

Type: Float
Default value: 0.1
Unit: Radian
Description: Maximum allowed angle of rotation of each molecule in one fbMC step.

TranslationStepLength

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Maximum allowed displacement of each molecule in each Cartesian coordinate in one fbMC step.

NSteps

Type: Integer
GUI name: Number of steps
Description: Number of fbMC steps to perform on every invocation of the procedure.

PrintFreq

Type: Integer
GUI name: Printing frequency
Description: Print current thermodynamic properties to the output every N fbMC steps. This defaults to the PrintFreq set in the Trajectory block. Setting this to zero disables printing fbMC steps.

StartStep

Type: Integer
Default value: 1
Description: First step at which the fbMC procedure may run.

StepLength

Type: Float
Default value: 0.1
Unit: Angstrom
Description: Maximum allowed displacement of the lightest atom in the system in each Cartesian coordinate in one fbMC step.

StopStep

Type: Integer
Default value: 0
Description: Last step at which the fbMC procedure may run. If unset or zero, there is no limit.

Temperature

Type: Float
Unit: Kelvin
Description: Temperature used for fbMC.

Nanoreactor¶

See also

The ReactionsDiscovery workflow uses the nanoreactor to predict chemical reactions.

Nanoreactor is implemented following the article by L.-P. Wang et al. 5. The nanoreactor is a spherical region of space centered at the origin and surrounded by an elastic wall (represented by a harmonic potential), its size changing over time. The idea of the nanoreactor is to have two phases: reaction and relaxation. In the following, each nanoreactor phase is referred to as a reactor. During the relaxation phase, the reactor is large and if the temperature is high enough the reactants are distributed more or less evenly throughout its volume. In the reaction phase, the reactor shrinks and the atoms that now fall outside the reactor’s sphere accelerate towards its center. During this phase, high-energy collisions may lead to reactions. After the reaction phase is over, the relaxation phase begins again and the reactor is expanded. This cycle is repeated indefinitely.

Each phase is specified by its own Reactor input block. There should be at least two of them but there can be more. The NSteps key specifies the duration of the phase in MD steps. The radius of the reactor and the force constant of its wall are set by the Radius and ForceConstant keys, respectively. To minimize additional strain on internal degrees of freedom of the affected molecules, the force applied by the wall on an atom is proportional to the atom’s mass by default. This means that atoms situated at the same distance from the center of the reactor will receive the same acceleration irrespective of their mass. This should be taken into account when choosing a value for the ForceConstant. Alternatively, this feature can be disabled using the MassScaled key.

MolecularDynamics

Reactor

Type: Block
Recurring: True
Description: Define one phase of the nanoreactor. A reactor is a region of space surrounded by an elastic wall. Atoms inside the region are not affected. Atoms outside it will be pushed back with force depending on the [ForceConstant] and the [MassScaled] flag.

ForceConstant

Type: Float
GUI name: Reactor force constant
Description: Force constant of the reactor wall in Hartree/Bohr^2 (or Hartree/Bohr^2/Dalton if [MassScaled] is true).

MassScaled

Type: Bool
Default value: Yes
GUI name: Scale force by mass
Description: If this flag is disabled the force on an atom outside of the reactor depends only on the atomic coordinates and the force constant. Otherwise, the force is also multiplied by the mass of the atom. This means that atoms at the same distance from the wall will receive the same accelerate due to the wall potential.

NSteps

Type: Integer
GUI name: Reactor lifetime
Description: Number of steps for which the reactor will remain active until disabled. The next reactor will be activated immediately after this. After the last reactor is disabled the cycle will repeat.

Radius

Type: Float
Unit: Angstrom
GUI name: Reactor radius
Description: Radius of the reactor sphere.

Non-equilibrium MD (NEMD)¶

T-NEMD for thermoconductivity: heat exchange¶

There are different methods to study thermal conductivity using non-equilibrium molecular dynamics (NEMD). A common feature of these methods is that they require the system to be divided into three or more zones, each with its own thermostat and other properties. One method maintains the temperature of the heat source and the heat sink zones at the given temperature using two different thermostats and measures the amount of heat transferred. These method does not require any special features besides a standard thermostat and a possibility to calculate the amount of heat accumulated by the thermostat per unit of time. The accumulated thermostat energies are available in the MDHistory section of ams.rkf file, in variables called ‘XXXXstat#Energy’, where XXXX is a 4-letter abbreviation of the thermo-/barostat (‘BerT’ for a Berendsen thermostat, ‘NHCT’ for an NHC thermostat, ‘NHTB’ for an MTK barostat, etc.) and ‘#’ is a 1-digit index of the thermo-/barostat.

In the other method, the heat flow is constant and the induced temperature gradient is measured. This method is implemented in AMS in three variants: a simple heat exchange, HEX 1 and eHEX 2. In the simple heat exchange method the atom velocities are scaled up (or down) by a factor corresponding to the amount of heat deposited to the heat source (or withdrawn from the heat sink) without paying attention to the conservation of the total momentum of the heat source (or sink). In the HEX method the velocities are scaled in such a way that the total momentum is conserved. This, however, introduces a small but measurable drift in the total energy. The eHEX algorithm improves upon the HEX by adding a third-order time-integration correction to remove the drift.

This method is controlled by the HeatExchange sub-block of the MolecularDynamics block:

MolecularDynamics

HeatExchange

Type: Block
Recurring: True
GUI name: Heat exchange
Description: Input for the heat-exchange non-equilibrium MD (T-NEMD).

HeatingRate

Type: Float
Unit: Hartree/fs
Description: Rate at which the energy is added to the Source and removed from the Sink. A heating rate of 1 Hartree/fs equals to about 0.00436 Watt of power being transferred through the system.

Method

Type: Multiple Choice
Default value: Simple
Options: [Simple, HEX, eHEX]
Description: Heat exchange method used. Simple: kinetic energy of the atoms of the source and sink regions is modified irrespective of that of the center of mass (CoM) of the region (recommended for solids). HEX: kinetic energy of the atoms of these regions is modified keeping that of the corresponding CoM constant. eHEX: an enhanced version of HEX that conserves the total energy better (recommended for gases and liquids).

Sink

Type: Block
Description: Defines the heat sink region (where the heat will be removed).

AtomList

Type: Integer List
GUI name: Sink region
Description: The atoms that are part of the sink. This key is ignored if the [Box] block or [Region] key is present.

Box

Type: Block
Description: Part of the simulation box (in fractional cell coordinates) defining the heat sink. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes.

Amax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the third axis.

Region

Type: String
GUI name: Sink region
Description: The region that is the sink. This key is ignored if the [Box] block is present.

Source

Type: Block
Description: Defines the heat source region (where the heat will be added).

AtomList

Type: Integer List
GUI name: Source region
Description: The atoms that are part of the source. This key is ignored if the [Box] block or [Region] key is present.

Box

Type: Block
Description: Part of the simulation box (in fractional cell coordinates) defining the heat source. If this block is specified, then by default, the whole box in each of the three dimensions is used, which usually does not make much sense. Normally, you will want to set the bounds along one of the axes. This block is mutually exclusive with the FirstAtom/LastAtom setting.

Amax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the first axis.

Amin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the first axis.

Bmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the second axis.

Bmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the second axis.

Cmax

Type: Float
Default value: 1.0
Description: Coordinate of the upper bound along the third axis.

Cmin

Type: Float
Default value: 0.0
Description: Coordinate of the lower bound along the third axis.

Region

Type: String
GUI name: Source region
Description: The region that is the source. This key is ignored if the [Box] block is present.

StartStep

Type: Integer
Default value: 0
Description: Index of the MD step at which the heat exchange will start.

StopStep

Type: Integer
Description: Index of the MD step at which the heat exchange will stop.

One should be careful when choosing a value for the HeatingRate because a too large value may lead to pyrolysis of the heat source or to an abnormal termination when all the kinetic energy of the heat sink has been drained. The optimal value depends on the size of the system, its heat conductivity and the desired temperature gradient value. The thermal conductivity k can be calculated by dividing the heat flow rate W by the temperature gradient grad(T) and by the flow cross-section area S: \(k = W/(S \cdot grad(T))\). See the trajectory sampling section above on how to obtain the temperature profile from which the grad(T) can be computed.

NEMD for tribology: Applying velocities / forces¶

Non-equilibrium Molecular Dynamics (NEMD) is a commonly used tool to study phenomena like friction & wear in tribochemical systems. In these MD simulations, an constant external force or velocity is applied to a specific subgroup of atoms. For example, when studying sliding solid surfaces, the ApplyForce feature can be used to exert a compressive normal force in the -Z direction on one of the solid slabs while the ApplyVelocity block simultaneously slides the same group of atoms along the X or Y axis.

In the case of ApplyVelocity, the specified group of atoms (defined as a Region) will move with the specified constant net Velocity. The imposed velocity is automatically excluded from thermostatting and system-wide momentum removal. The Components input key can be used to select just a subset of Cartesian components of the net velocity of the group to be controlled, so that other components can be left to evolve freely. In the sliding example in the previous paragraph, one would use Components=XY to let the Z motion of the sliding slab to freely follow the applied normal force.

In the case of ApplyForce, the selected Region (group of atoms) will experience an additional specified constant Force on each timestep of the simulation. By default, the Force parameter defines the total (net) force acting on the whole Region. This can be changed by setting the PerAtom option to apply the Force to each atom in the Region separately.

MolecularDynamics

ApplyVelocity

Type: Block
Recurring: True
Description: The ApplyVelocity keyword can be used to move an arbitrary group of atoms in the system with a constant net velocity

Components

Type: Multiple Choice
Default value: XY
Options: [X, Y, Z, XY, YZ, XZ, XYZ]
Description: Select which components of the Velocity vector are used to set the corresponding components of the net velocity of the specified set of atoms. Any other components of Velocity are ignored and the motion of the selected atoms in those directions is unaffected by ApplyVelocity.

Region

Type: String
Recurring: True
Description: Applies the defined velocity to all atoms in this region.

Velocity

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Angstrom/fs
Recurring: False
Description: The constant velocity that will be applied to the specified atoms.

MolecularDynamics

ApplyForce

Type: Block
Recurring: True
Description: The ApplyForce keyword can be used to apply an arbitrary constant force to a certain (subgroups of) atoms in the system

Force

Type: Float List
Default value: [0.0, 0.0, 0.0]
Unit: Hartree/Bohr
Description: Defines the constant force vector

PerAtom

Type: Bool
Default value: No
Description: If enabled, the Force vector is applied separately to every atom in the selected Region, so that the total net force on the Region equals the value of Force times the number of atoms in Region. This was the behavior of ApplyForce in AMS2022. By default, with PerAtom disabled, the Force vector defines the total net force on the Region, so the force applied to each atom equals the value of Force divided by the number of atoms in Region.

Region

Type: String
Recurring: True
Description: Apply the constant force to all atoms in this region.

When the ApplyVelocity block is used to slide a region, the measured net force experienced by that region is written to the MDHistory section on the trajectory. This force is calculated directly from the gradients returned by an Engine and thus excludes the effect of any ApplyForce blocks. The ratio of the tangential (sliding) and normal (compression) component of the mean force is thus equal to the friction coefficient. Three variables will be written by any ApplyVelocity block:

EngXFrcRgnA: instantaneous engine force on region A, Cartesian component X
MeanEngXFrcRgnA: average of EngXFrcRgnA over all timesteps since the previous trajectory frame
StdevEngXFrcRgnA: standard deviation of EngXFrcRgnA over all timesteps since the previous trajectory frame

Note

Only the first eight characters of the region name are used to construct the EngXFrcRgn variables. When using multiple ApplyVelocity instances with different regions, make sure their names are not ambiguous after shortening to eight characters.

NEMD viscosity via cosine shear perturbation¶

In order to calculate the viscosity using NEMD, apply a periodic perturbation to the system using the CosineShear input block. This will add an amount of acceleration to the atoms in the system according to a cosine function running along the specified Cartesian ProfileAxis. The acceleration applied to each atom will have the direction of FlowDirection and magnitude equal to \(a_x(z) = A \cos(\frac{2 \pi z}{L_z})\), where A is the amplitude defined by the Acceleration input key and L_z is the length of the periodic box in the Z axis (assuming ProfileAxis=Z and FlowDirection="1 0 0". It is typically the most efficient to use a box roughly three times taller in the ProfileAxis direction than in the other two axes. AMS currently requires the ProfileAxis to be aligned with one of the lattice vectors and perpendicular to the remaining lattice vectors.

Warning

CosineShear simulations are typically performed in the NVT ensemble. While using a Barostat is theoretically possible, such a combination has not been physically validated by SCM.

MolecularDynamics

CosineShear

Type: Block
Description: Apply an external acceleration to all atoms of a fluid using a periodic (cosine) function along a selected coordinate axis. This induces a periodic shear flow profile which can be used to determine the viscosity.

Acceleration

Type: Float
Default value: 5e-06
Unit: Angstrom/fs^2
Description: Amplitude of the applied cosine shear acceleration profile. The default value should be a rough first guess for water and it needs to be adjusted by experimentation for other systems.

Enabled

Type: Bool
Default value: No
GUI name: Enable cosine shear
Description: Apply a cosine shear acceleration profile for a NEMD calculation of viscosity.

FlowDirection

Type: Float List
Default value: [1.0, 0.0, 0.0]
Description: The direction in which to apply the shear acceleration, in Cartesian coordinates. The magnitude of this vector is ignored (AMS will normalize it internally). FlowDirection has to be perpendicular to ProfileAxis.

ProfileAxis

Type: Multiple Choice
Default value: Z
Options: [X, Y, Z]
Description: The Cartesian coordinate axis along which the cosine wave runs

This generates a velocity profile in the steady state that looks like: \(v_x(z) = V \cos(\frac{2 \pi z}{L_z})\). After the system reaches a steady state, the velocity amplitude V will be approximately constant, although typically relatively noisy. Averaging V over a long enough trajectory yields a reasonable estimate of the steady-state flow velocity, which can then be used to calculate the viscosity as \(\eta = \frac{A \rho L_z^2}{4 \pi^2}\). The measured value of V averaged over every Trajectory SamplingFreq timesteps is written to the trajectory as MeanCosineShearVelocity in the units of Bohr/fs.

The calculated viscosity value will be different from the equilibrium viscosity of the studied liquid due to shear thinning and heating caused by the applied acceleration A. It is thus necessary to measure the viscosity at several different values of A and extrapolate the obtained values to the zero-shear limit \(A = 0\). To do this, it is useful to calculate the “shear parameter” \(S = \frac{A^2 m \rho L_z^2}{8 \pi^2 N_f k_B}\), where m is the total mass of the system and N_f is the number of degrees of freedom. The measured viscosity \(\eta\) is then approximately a linear function of S, enabling a straightforward extrapolation to zero S. Typical values of the shear parameter S in SI units are on the order of 10⁹ - 10¹⁰ kg m s⁻² K.

Applying reflective walls¶

Note

This feature is still experimental. It may contain bugs and some input keys are still subject to change in future releases of AMS. If you are interested in trying it out, monitor the bug fix changelog for updates and feel free to get in touch with us at support@scm.com if you run into any issues.

The ReflectiveWall keyword can be used to define impenetrable planes in space, causing molecules to bounce off by an elastic collision. Therefore, the main usage of reflective walls is to make sure that molecules will stay within a certain area in space.

The reflective wall is defined by a normal vector (Axis) and a Threshold. The plane of the wall is perpendicular to Axis and passes through a point given by multiplying Axis by Threshold. Any atom moving in the direction of Axis will be reflected back, but the opposite does not apply. Particles moving in the direction opposite to Axis will not be affected (the wall works like a one-way mirror). The Axis vector does not need to be normalized to unity, AMS will normalize it internally and adjust Threshold accordingly.

MolecularDynamics

ReflectiveWall

Type: Block
Recurring: True
Description: Apply a reflective wall in space

Axis

Type: Float List
Unit: Angstrom
Description: Defines the normal vector perpendicular to the plane of the reflective wall. Any particle moving in this direction will be reflected back.

Region

Type: String
Recurring: True
Description: Apply the reflective wall to all atoms in this region.

Threshold

Type: Float
Unit: Angstrom
Description: Defines the threshold value determining the position of the reflective wall. If the dot product of a position of a particle with Axis exceeds Threshold, the particle will be reflected. This means that the plane of the wall passes through a point given by Axis times Threshold.

Exit Conditions¶

It is possible to define exit conditions to end a molecular dynamics calculations before all timesteps have been performed. If an exit condition is met, the variable History%ExitConditionMsg is populated with a message describing why the molecular dynamics task was stopped. When an exit condition is met, its status is considered to be NORMAL TERMINATION.

ExitCondition
   AtomsTooClose
      MinimumDistance float
      PairCalculation [NeighborList | DistanceMatrix]
   End
   EngineEnergyUncertainty
      MaxUncertainty float
      Normalization float
   End
   EngineGradientsUncertainty
      MaxUncertainty float
   End
   Type [AtomsTooClose | EngineEnergyUncertainty | EngineGradientsUncertainty]
End

ExitCondition

Type: Block
Recurring: True
Description: If any of the specified exitconditions are met, the AMS driver will exit cleanly.

AtomsTooClose

Type: Block
Description: If any pair of atoms is closer than the specified minimum value, the program will exit cleanly.

MinimumDistance

Type: Float
Default value: 0.7
Unit: Angstrom
Description: Two atoms closer than this threshold value are considered too close.

PairCalculation

Type: Multiple Choice
Default value: NeighborList
Options: [NeighborList, DistanceMatrix]
Description: Two atoms closer than this threshold value are considered too close.

EngineEnergyUncertainty

Type: Block
Description: If the engine reports an uncertainty that is too high, the program will exit cleanly.

MaxUncertainty

Type: Float
Default value: 0.001
Unit: Hartree
Description: Threshold for Engine Energy Uncertainty divided by Normalization (by default the number of atoms)

Normalization

Type: Float
Value Range: value >= 0.0
Description: Divide the reported Engine Energy Uncertainty by this normalization. Will divide by the number of atoms if unset.

EngineGradientsUncertainty

Type: Block
Description: If the engine reports an uncertainty in the magnitude of the nuclear gradient of any atom that is too high, the program will exit cleanly.

MaxUncertainty

Type: Float
Default value: 0.01580221
Unit: Hartree/Angstrom
Description: Threshold for Engine Gradients Uncertainty.

Type

Type: Multiple Choice
Default value: AtomsTooClose
Options: [AtomsTooClose, EngineEnergyUncertainty, EngineGradientsUncertainty]
Description: The type of exitcondition specified

References

1: T. Ikeshoji and B. Hafskjold, Non-equilibrium molecular dynamics calculation of heat conduction in liquid and through liquid-gas interface Molecular Physics 81, 251-261 (1994)
2: P. Wirnsberger, D. Frenkel, and C. Dellago, An enhanced version of the heat exchange algorithm with excellent energy conservation properties Journal of Chemical Physics 143, 124104 (2015)
3: A. Vashisth, C. Ashraf, W. Zhang, C.E. Bakis, and A.C.T. van Duin, Accelerated ReaxFF simulations for describing the reactive cross-linking of polymers, J. Phys. Chem. A, 122, 6633-6642 (2018)
4: M.J. Mees, G. Pourtois, E. C. Neyts, B. J. Thijsse, and André Stesmans, Uniform-acceptance force-bias Monte Carlo method with time scale to study solid-state diffusion, Phys. Rev. B 85, 134301 (2012)
5: L.-P. Wang, A. Titov, R. McGibbon, F. Liu, V.S. Pande and T.J. Martínez, Discovering chemistry with an ab initio nanoreactor, Nature Chemistry 6, 1044 (2014)
6: He Huang, E. Ozkirimli, C.B. Post, A Comparison of Three Perturbation Molecular Dynamics Methods for Modeling Conformational Transitions, J Chem Theory Comput. 5 (2009) 1301–1314

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Molecular dynamics¶

General¶

Constrained molecular dynamics¶

(Re-)Starting a simulation¶

Thermostats and barostats¶

Temperature and pressure regimes¶

Trajectory sampling and output¶

Lattice deformations (volume regimes)¶

Molecule Gun: adding molecules during simulation¶

Removing molecules during simulation¶

Accelerated dynamics¶

The PLUMED library support in AMS¶

Metadynamics for Conformer-Rotamer Ensemble Sampling (CREST-MTD)¶

Collective Variable-driven HyperDynamics (CVHD)¶

Temperature Replica Exchange¶

Bond Boost Method¶

Reaction boost (Targeted MD)¶

Force bias Monte Carlo (fbMC)¶

Nanoreactor¶

Non-equilibrium MD (NEMD)¶

T-NEMD for thermoconductivity: heat exchange¶

NEMD for tribology: Applying velocities / forces¶

NEMD viscosity via cosine shear perturbation¶

Applying reflective walls¶

Exit Conditions¶