Molecular dynamics

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

See also

• Examples
• AMS GUI Tutorial
• MD trajectory analysis tool

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
      Coords float_list
      CoordsBox float_list
      CoordsSigma float_list
      Energy float
      EnergySigma float
      FractionalCoords float_list
      FractionalCoordsBox float_list
      FractionalCoordsSigma float_list
      Frequency integer
      MinDistance float
      NumAttempts integer
      Rotate [True | False]
      StartStep integer
      StopStep integer
      System string
      Temperature float
      TemperatureSigma float
      Velocity float
      VelocityDirection float_list
      VelocitySigma float
   End
   Barostat
      BulkModulus float
      ConstantVolume [True | False]
      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
   BondOrderCutoff float
   CVHD
      Bias
         DampingTemp float
         Delta float
         Height float
      End
      ColVarBB
         at1 string
         at2 string
         cutoff float
         p integer
         rmax float
         rmin float
      End
      Frequency integer
      StartStep integer
      StopStep integer
      WaitSteps integer
   End
   CalcPressure [True | False]
   Checkpoint
      Frequency integer
   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
         FirstAtom integer
         LastAtom integer
      End
      Source
         AtomList integer_list
         Box
            Amax float
            Amin float
            Bmax float
            Bmin float
            Cmax float
            Cmin float
         End
         FirstAtom integer
         LastAtom integer
      End
      StartStep integer
      StopStep integer
   End
   InitialVelocities
      File string
      Temperature float
      Type [Zero | Random | FromFile | Input]
      Values # Non-standard block. See details.
         ...
      End
   End
   NSteps integer
   Plumed
      Input # Non-standard block. See details.
         ...
      End
   End
   Preserve
      AngularMomentum [True | False]
      CenterOfMass [True | False]
      Momentum [True | False]
   End
   Print
      System [True | False]
      Velocities [True | False]
   End
   RemoveMolecules
      Formula string
      Frequency integer
      SafeBox
         Amax float
         Amin float
         Bmax float
         Bmin float
         Cmax float
         Cmin float
      End
      SinkBox
         Amax float
         Amin float
         Bmax float
         Bmin float
         Cmax float
         Cmin float
      End
      StartStep integer
      StopStep integer
   End
   ReplicaExchange
      AllowWrongResults [True | False]
      EWMALength integer
      SwapFrequency integer
      TemperatureFactors float_list
      Temperatures float_list
      nReplicas integer
   End
   Restart string
   Thermostat
      BerendsenApply [Local | Global]
      ChainLength integer
      Duration integer_list
      FirstAtom integer
      LastAtom integer
      Tau float
      Temperature float_list
      Type [None | Berendsen | NHC]
   End
   TimeStep float
   Trajectory
      SamplingFreq integer
      TProfileGridPoints integer
   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:True GUI name:: Angular momentum Description:Remove overall angular momentum of the system. This option is ignored for 2D and 3D-periodic systems.

CenterOfMass

Type:Bool Default value:False 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:True GUI name:Preserve: Total momentum Description:Remove overall (linear) momentum of the system.

Constrained molecular dynamics

It is possible to keep part of the system frozen in place during MD. This is achieved using the Atom or AtomList 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.

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.

(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 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.

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. ADFinput 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 ADFinput.

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 regions of the system at the same time. This is done by specifying the Thermostat block multiple times and setting the FirstAtom and/or LastAtom keys to the desired range of atoms. Care needs to be taken to avoid defining thermostats with overlapping atom ranges.

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.

FirstAtom

Type:Integer Default value:1 Description:Index of the first atom to be thermostatted

LastAtom

Type:Integer Default value:0 Description:Index of the last atom to be thermostatted. A value of zero means the last atom in the system.

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:False 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:

1. Increase linearly from 0 to 300 K over 100 steps.
2. Stay constant at 300 K for 200 steps.
3. Increase linearly from 300 to 500 K over 100 steps.
4. Stay constant at 500 K for 200 steps.
5. Decrease linearly from 500 to 300 K over 100 steps.
6. 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.

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.

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 is greater than 0 then a temperature profile will be generated along each of the three unit cell axes. By default, no profile is generated.

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.

CalcPressure

Type:Bool Default value:False 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:False Description:Print the chemical system before and after the simulation.

Velocities

Type:Bool Default value:False Description:Print the atomic velocities before and after the simulation.

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. The total momentum of the added molecule is not conserved.

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 ADFinput, 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.

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.

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:False 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. ADFinput 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 TemperatureSigma.

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 ADFinput 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.

Removing molecules during simulation

This feature can be used, for example, to remove reaction products from the system.

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.

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 a 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 atomic units.

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.

SinkBox

Type:Block Description:Part of the simulation box where molecules will be removed. By default, molecules matching the formula will be removed regardless of their location. If this block is present a molecule will 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 atomic units.

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.

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.

BondOrderCutoff

Type:Float Default value:0.5 Description:Bond order cutoff for analysis of the molecular composition. Bonds with bond order smaller than this value are neglected when determining the molecular composition.

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.

Input

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

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: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: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.

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].

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.

Non-equilibrium MD (NEMD): 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 Berendset 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 transfered 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 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. 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.

FirstAtom

Type:Integer Description:Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.

LastAtom

Type:Integer Description:Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key 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 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.

FirstAtom

Type:Integer Description:Index of the first atom of the region. This key is ignored if the [Box] block or the [AtomList] key is present.

LastAtom

Type:Integer Description:Index of the last atom of the region. This key is ignored if the [Box] block or the [AtomList] key 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.

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:False 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 ADFmovie. 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.

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)