Molecular dynamics¶

To enable the molecular dynamics, set MolecularDynamics%Enabled to Yes. If it is set to No, you can still load previously run MD simulations and continue with the Network Extraction and Product Ranking parts.

The reactions discovery tool implements special non-equilibrium MD methods to promote chemical reactions, namely the Nanoreactor and Lattice deformation. The type is controlled by MolecularDynamics%Type.

The number of simulations to run is controlled by MolecularDynamics%NumSimulations. To get enough statistics, it is recommended to run several MD simulations. The results will be gathered into a single summary in the Network Extraction and Product Ranking parts.

To replace all hydrogens with deuterium set MolecularDynamics%UseDeuterium Yes. If you prefer, you can use a bond guessing algorithm instead of the engine-calculated bonds by setting MolecularDynamics%BondOrders%Method to Guess.

Nanoreactor¶

To enable the nanoreactor mode, set MolecularDynamics%Type to NanoReactor.

The nanoreactor is run without periodic boundary conditions. Details can be found in the Nanoreactor AMS Driver documentation.

The following 4 phases are looped throughout the simulation:

phase	volume fraction	time (fs)	thermostat T (K)	force constant (Ha/bohr^2)
pre_compression	1.05	25	250	0.0005
compression	`MinVolumeFraction`	25	250	0.01
post_compression	1.05	100	250	0.0005
diffusion	1.05	`DiffusionTime`	`Temperature`	0.0004

The radius of the nanoreactor for each individual phase is calculated as:

r_nanoreactor (per phase) = volume fraction^1/3 * InitialRadius

InitialRadius is automatically determined, but can also be explicitly specified in the input.

If you want to customize any numbers other than MinVolumeFraction, DiffusionTime, and Temperature, or if you want to change the number of phases, you can

set up your own NanoReactor simulations outside the Reactions Discovery tool, and then
specify the path to the results using NetworkExtraction.

All nanoreactor-specific input options:

MolecularDynamics
   NanoReactor
      DiffusionTime float
      InitialRadius float
      MinVolumeFraction float
      NumCycles integer
      Temperature float
   End
End

MolecularDynamics

Type: Block
Description: Settings for reactive molecular dynamics.

NanoReactor

Type: Block
Description: Option for the reactive molecular dynamics.

DiffusionTime

Type: Float
Default value: 250.0
Unit: fs
Description: The length of the diffusion phase in femtoseconds.

InitialRadius

Type: Float
Unit: angstrom
Description: The radius of the initial (spherical) system. If BuildSystem is used, the value is ignored (then the value is automatically determined). If BuildSystem is not used, then a guess for the InitialRadius will be made if it is not specified.

MinVolumeFraction

Type: Float
Default value: 0.6
GUI name: Minimum volume fraction
Description: The minimum (compressed) volume of the system, as a fraction of the initial (maximum) system volume.

NumCycles

Type: Integer
Default value: 10
GUI name: Number of cycles
Description: How many compression-expansion cycles to perform.

Temperature

Type: Float
Default value: 500.0
Unit: K
Description: Temperature during the diffusion phase. The temperature during the compression phase will be much higher as a result of the inward acceleration.

Lattice deformation¶

To enable the lattice deformation mode, set MolecularDynamics%Type to LatticeDeformation.

Lattice deformation requires that the system is 3D-periodic. For more details, see the Lattice deformations (volume regimes) AMS Driver documentation.

The volume oscillates for NumCycles cycles with a period of Period fs between

V_initial, and
V_compressed = V_initial* MinVolumeFraction.

All lattice deformation input options:

MolecularDynamics
   LatticeDeformation
      MinVolumeFraction float
      NumCycles integer
      Period float
      Temperature float
   End
End

MolecularDynamics

Type: Block
Description: Settings for reactive molecular dynamics.

LatticeDeformation

Type: Block
Description: Option for the reactive molecular dynamics.

MinVolumeFraction

Type: Float
Default value: 0.3
GUI name: Minimum volume fraction
Description: The minimum (compressed) volume of the system, as a fraction of the initial (maximum) system volume.

NumCycles

Type: Integer
Default value: 10
GUI name: Number of cycles
Description: How many compression-expansion cycles to perform.

Period

Type: Float
Default value: 100.0
Unit: fs
Description: The period with which the lattice will oscillate in femtoseconds.

Temperature

Type: Float
Default value: 500.0
Unit: K
Description: Thermostat temperature during the MD simulation.

Build the initial system¶

Note

This section describes a convenient way to build the system directly from the input.

You can also build the initial system in any way you like. Then set MolecularDynamics%BuildSystem%Enabled to False and give the coordinates/lattice or coordinate file in the System block.

BuildSystem will build a

sphere centered at the origin if MolecularDynamics%Type is NanoReactor - the radius of the sphere will automatically be passed on to the NanoReactor settings.
cubic box if MolecularDynamics%Type is LatticeDeformation.

The initial system is specified through a series of Molecule blocks. Each Molecule block contains either a SMILES string or a reference to a System block, as well as the mole fraction of that particular molecule.

The initial density and the system size are specified with the Density and NumAtoms keywords:

You can choose to run a short equilibration simulation by setting Equilibration. This can be useful if the packmol-generated structure is unrealistic.

MolecularDynamics
   BuildSystem
      Density float
      Enabled Yes/No
      Equilibration Yes/No
      Molecule
         MoleFraction float
         SMILES string
         SystemID string
      End
      NumAtoms integer
   End
End

MolecularDynamics

Type: Block
Description: Settings for reactive molecular dynamics.

BuildSystem

Type: Block
Description: Build the initial system for molecular dynamics with packmol. If MolecularDynamics%Type is set to Restart, then BuildSystem is ignored.

Density

Type: Float
Default value: 1.0
Unit: g/cm^3
Description: The initial density of the system. This should be the lowest density (corresponding to the largest volume) that you want the system to have. The standard atomic masses are used when building the system.

Enabled

Type: Bool
Default value: Yes
GUI name: Build System
Description: If True, build the initial system using packmol. If False, a System block must be provided with the initial system.

Equilibration

Type: Bool
Default value: No
Description: Whether to run a short 250 fs equilibration simulation on the packmol-built structure.

Molecule

Type: Block
Recurring: True
Description: A molecule to put in the MD simulation.

MoleFraction

Type: Float
Default value: 1.0
GUI name: Relative mole fraction
Description: Mole fraction of the molecule (the mole fractions of the various molecules will be normalized, so only the relative MoleFraction values matter)

SMILES

Type: String
Description: The SMILES string of the molecules.

SystemID

Type: String
Description: The ID of the corresponding System (i.e. the header of the corresponding System block).

NumAtoms

Type: Integer
Default value: 200
GUI name: Number of atoms
Description: Approximate total number of atoms in each MD simulation.

Fixed MD settings¶

The reactions discovery tool automatically sets the following for all MD simulations:

Short-range repulsive potential,
Frames are saved every 10 fs. To save disk space, velocities are not saved.
MD checkpoints are saved every 1000 MD steps (allowing to Restart)
A Berendsen thermostat with a very short time constant and BerendsenApply = Local.

For a complete view of all the MD input, open the mdsim_0/mdsim_0.in file created by the Reactions Discovery tool.

Molecular dynamics restart¶

Set MolecularDynamics Type=Restart in order to

continue interrupted MD simulations (for example if they exceeded the walltime limit), or
add extra steps to already finished MD simulations

MolecularDynamics
   Restart
      Directory string
      NSteps integer
   End
End

MolecularDynamics

Type: Block
Description: Settings for reactive molecular dynamics.

Restart

Type: Block
Description: Settings for restarting MD simulations.

Directory

Type: String
GUI name: Restart directory
Description: Directory containing a previous Reactions Discovery calculation with MD simulations that were not finished. Note: This directory will be scanned recursively for ams.rkf files!

NSteps

Type: Integer
GUI name: Number of steps
Description: Number of MD steps. If left empty, the number of MD steps from the original MD trajectory will be used. Note that you need to manually increase this number if you want to continue finished simulations.

Example: restart MD simulations after they exceeded walltime limit¶

Input:

MolecularDynamics
    Enabled Yes
    Type Restart
    Restart
        Directory /some/path
    End
End
Engine ...
    ...
EndEngine

If /some/path contains the following files:

/some/path/dir1/ams.rkf
/some/path/dir2/subdir/ams.rkf

where those ams.rkf files come from MD simulations, then if

ams.rkf contains an unfinished simulation (e.g. because the job exceeded the walltime limit), it will be restarted from where it finished, but if
ams.rkf contains a finished simulation, then the trajectory will simply be copied

Note

The rest of the MolecularDynamics reactions discovery input block is ignored, meaning that it doesn’t matter if you specify LatticeDeformation or NanoReactor or their respective settings. The MD settings from the ams.rkf file will be used.
The Engine block from the reactions discovery input block is used.
If you restart from a previous reactions discovery results directory (which you likely do), then it may contain several directories mdsim_0, mdsim_1, etc., or you may have called them something else if you set up the MD simulations manually. The numbering may change in the restart run, so that the new mdsim_1 actually continues the trajectory from the original mdsim_0.

Example: Continue MD simulations for more steps¶

MolecularDynamics
    Enabled Yes
    Type Restart
    Restart
        Directory /some/path
        NSteps 20000
    End
End
Engine ...
    ...
EndEngine

The above will continue all MD simulations until 20000 steps. If the original simulation ran for 5000 steps, then the new simulation will continue for another 15000 steps.