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.
See also
MolecularDynamics
Enabled Yes/No
Type [NanoReactor | LatticeDeformation | Restart]
NumSimulations integer
UseDeuterium Yes/No
TimeStep float
BondOrders
Method [Guess | EngineWithGuessFallback]
End
End
MolecularDynamics- Type:
Block
- Description:
Settings for reactive molecular dynamics.
Enabled- Type:
Bool
- Default value:
Yes
- GUI name:
Reactive Molecular Dynamics
- Description:
Whether to run molecular dynamics.
Type- Type:
Multiple Choice
- Default value:
NanoReactor
- Options:
[NanoReactor, LatticeDeformation, Restart]
- Description:
The type of molecular dynamics.
NumSimulations- Type:
Integer
- Default value:
4
- GUI name:
Number of simulations
- Description:
Total number of MD simulations to run.
UseDeuterium- Type:
Bool
- Default value:
No
- Description:
If true, all hydrogen atoms will be replaced by deuterium during the MD. This helps to slow down the motion of the hydrogen atoms. This options does *not* affect the density you should insert in BuildSystem%Density. However, it *does* affect the density on the resulting MD trajectory file.
TimeStep- Type:
Float
- Default value:
0.5
- Unit:
fs
- Description:
Molecular dynamics time step.
BondOrders- Type:
Block
- Description:
Details regarding the calculation/guessing of bond orders during Molecular Dynamics. The bond changes during the MD are later analyzed in the Network Extraction step.
Method- Type:
Multiple Choice
- Default value:
EngineWithGuessFallback
- Options:
[Guess, EngineWithGuessFallback]
- Description:
How to compute the bond orders. ‘Guess’: Use a bond guessing algorithm based on the system’s geometry. This is the same algorithm that is used by the Graphical User Interface to guess bonds. ‘EngineWithGuessFallback’: let the engine compute the bond orders but if the engine did not produce any bond orders, use the bond guessing algorithm as a fallback option.
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 |
|
25 |
250 |
0.01 |
post_compression |
1.05 |
100 |
250 |
0.0005 |
diffusion |
1.05 |
|
|
0.0004 |
The radius of the nanoreactor for each individual phase is calculated as:
rnanoreactor (per phase) = volume fraction1/3 *
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
BuildSystemis used, the value is ignored (then the value is automatically determined). IfBuildSystemis not used, then a guess for theInitialRadiuswill 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
Vinitial, and
Vcompressed = Vinitial*
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%TypeisNanoReactor- the radius of the sphere will automatically be passed on to theNanoReactorsettings.cubic box if
MolecularDynamics%TypeisLatticeDeformation.
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%Typeis set toRestart, 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:
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.
See also
Molecular dynamics in the AMS Driver documentation
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
MolecularDynamicsreactions discovery input block is ignored, meaning that it doesn’t matter if you specifyLatticeDeformationorNanoReactoror their respective settings. The MD settings from theams.rkffile will be used.The
Engineblock 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 newmdsim_1actually continues the trajectory from the originalmdsim_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.