Keywords¶
Links to manual entries¶
forcefield:
Summary of all keywords¶
Engine ForceField¶
AllowMissingParameters
- Type:
Bool
- Default value:
No
- Description:
When parameters are not found for bonds, angles, dihedrals, or inversions, the first entry in the database will be used.
AntechamberIntegration
- Type:
Bool
- Default value:
No
- GUI name:
Automatic atom typing
- Description:
EXPERIMENTAL: Use the Antechamber program to automatically determine atom types for the GAFF force field. This may run a geometry optimization with MOPAC under the hood in order to determine the charges (see keyword AntechamberTask), which might not work for very large systems.
AntechamberTask
- Type:
Multiple Choice
- Default value:
GeometryOptimization
- Options:
[GeometryOptimization, SinglePoint]
- Description:
If antechamber is invoked to guess atomtypes and charges (GAFF force field), select the task for charge guessing with MOPAC
APPLE&P
- Type:
Block
- Description:
Options for the APPLE&P force field.
LongRangeCorrection
- Type:
Bool
- Default value:
Yes
- GUI name:
Add long-range correction
- Description:
Add a long-range dispersion correction to the energy and pressure for 3D-periodic systems.
This correction should be enabled only for a homogeneous liquid.
MuMu14Scaling
- Type:
Float
- Default value:
1.0
- GUI name:
Mu-Mu 3rd-neighbor scaling
- Description:
Scaling factor for dipole-dipole interactions between atoms connected to 3rd order (via a dihedral).
QMu14Scaling
- Type:
Float
- Default value:
0.2
- GUI name:
Q-Mu 3rd-neighbor scaling
- Description:
Scaling factor for charge-dipole interactions between atoms connected to 3rd order (via a dihedral).
QQ14Scaling
- Type:
Float
- Default value:
1.0
- GUI name:
Q-Q 3rd-neighbor scaling
- Description:
Scaling factor for charge-charge interactions between atoms connected to 3rd order (via a dihedral).
RD14Scaling
- Type:
Float
- Default value:
1.0
- GUI name:
RD 3rd-neighbor scaling
- Description:
Scaling factor for repulsion/dispersion interactions between atoms connected to 3rd order (via a dihedral).
BondsUsage
- Type:
Multiple Choice
- Default value:
Auto
- Options:
[Input, None, Guess, Auto]
- Description:
Controls what bonds are used by the engine. The choice auto means: guess in case there are no bonds. Guessing only happens at the first MD step, or first geometry optimization step.
CheckDuplicateRules
- Type:
Bool
- Default value:
Yes
- Description:
The database could contain duplicate entries. For torsions this is a feature, and the potentials will be added. For all other terms this is no allowed, and if detected the program stops. One should fix the database or set the checking to false. As always the last entry will be used.
DipoleConvergenceThreshold
- Type:
Float
- Default value:
1e-06
- Unit:
eBohr
- Description:
Convergence criterion for induced point dipoles, in atomic units. When the length of every atomic delta_mu vector between two iterations becomes below the tolerance, the procedure is considered converged.
DoChargeCheck
- Type:
Bool
- Default value:
No
- Description:
Check that the sum of atomic (partial) charges equals the total charge of the system.
EnergyTerms
- Type:
Block
- Description:
expert key, that allows you to disable specific energy terms.
Angle
- Type:
Bool
- Default value:
Yes
- Description:
Whether to use angle (bend) energy.
Coulomb
- Type:
Bool
- Default value:
Yes
- Description:
Whether to use coulomb energy.
Dispersion
- Type:
Bool
- Default value:
Yes
- Description:
Whether to use dispersion energy.
Inversion
- Type:
Bool
- Default value:
Yes
- Description:
Whether to use inversion energy.
Stretch
- Type:
Bool
- Default value:
Yes
- Description:
Whether to use stretch energy.
Torsion
- Type:
Bool
- Default value:
Yes
- Description:
Whether to use torsion energy.
EngineConstraints
- Type:
Bool
- Default value:
Yes
- Description:
Set to false to ignore constraints implied by the engine.
EwaldSummation
- Type:
Block
- Description:
Configures the details of the particle mesh Ewald (PME) summation of the Coulomb interaction.
Alpha
- Type:
Float
- Default value:
-1.0
- Unit:
1/Angstrom
- Description:
This parameter shifts the workload from real space (smaller alpha) to reciprocal space (larger alpha). Using a larger [Alpha] without decreasing [GridSpacing] may increase the error in the reciprocal-space contribution. Set to zero to disable the reciprocal-space Ewald part. Negative value means the [Alpha] will be determined automatically from the [Tolerance] and [RealSpaceCutoff] values.
Enabled
- Type:
Bool
- Default value:
Yes
- Description:
Set to false to use real-space pair summation instead of the Ewald, which is the default and the only option for molecules, 1D and 2D periodic systems.
GridSpacing
- Type:
Float
- Default value:
0.5
- Unit:
Angstrom
- Description:
Grid spacing in the particle mesh Ewald method. Smaller grid spacing will make the reciprocal energy calculation more accurate but slower. Using a larger [Alpha] value may require a smaller GridSpacing to be accurate.
RealSpaceCutoff
- Type:
Float
- Default value:
0.0
- Unit:
Angstrom
- Description:
Set the cutoff value for the real-space summation. Zero means the internal defaults will be used depending on the [Alpha] (if Alpha=0 then the cutoff will be set to 50 Bohr, otherwise to 20 Bohr).
Tolerance
- Type:
Float
- Default value:
1e-10
- Description:
Value of the error function that should be used to determine the cutoff radius for real-space Ewald summation if [Alpha] is set on input. Alternatively, if the [RealSpaceCutoff] is set but [Alpha] is not then the [Tolerance] value affects the [Alpha]. Larger values will make the real-space summation faster but less accurate.
ForceFieldFile
- Type:
String
- Default value:
- GUI name:
Force field library
- Description:
Path to the force field parameter file
GAFF
- Type:
Block
- Description:
Specific keywords for the GAFF force field type
ForceFieldPatchFile
- Type:
String
- Recurring:
True
- GUI name:
Force field patch file
- Description:
Path to the force field patch parameter file (additional parameters, missing from main file). Cannot be used when atomtypes are guessed.
GuessCharges
- Type:
Bool
- Default value:
No
- Description:
Use another engine to calculate/guess the charges to be used by the force field.
GuessChargesConfig
- Type:
Block
- Description:
Guess charges to be used by the forcefield
EngineType
- Type:
String
- Default value:
dftb
- Description:
Engine that can calculate or guess charges
KeepAntechamberFolder
- Type:
Bool
- Default value:
No
- Description:
If atom-typing is performed with antechamber, keep the folder after the call to antechamber
LAMMPSOffload
- Type:
Block
- Description:
Offload the calculation to LAMMPS via AMSPipe.
Enabled
- Type:
Bool
- Default value:
No
- Description:
Enable offloading the force field evaluation to LAMMPS instead of handling it internally in AMS. This is currently only supported for Type=UFF.
Input
- Type:
Block
- Description:
Commands to be passed to LAMMPS to set up the calculation. If this is left empty, AMS will generate a set of commands to set LAMMPS up according to the settings of the ForceField engine. Any LAMMPS commands entered in this input block will be used to set LAMMPS up instead of those generated by AMS. To merge the AMS-generated lines with your customizations, include lines like ‘AMS somelammpskeyword’ anywhere in this block. Any such line will be replaced by the AMS-generated line for ‘somelammpskeyword’. Any text after ‘somelammpskeyword’ will be appended to the generated line verbatim, which can be used to modify the generated command by additional options. A special line ‘AMS everything’ will be replaced by the entire block of AMS-generated commands, except those overridden anywhere in this input block (defined manually or inserted using ‘AMS somelammpskeyword’. Any customized Input block should probably include ‘AMS read_data’ near or at the end to load the AMS-generated data file defining the system.
UseGPU
- Type:
Bool
- Default value:
No
- Description:
Accelerate LAMMPS calculations using a GPU. Requires a LAMMPS library built with the GPU package.
UseGPUForKSpace
- Type:
Bool
- Default value:
Yes
- Description:
When UseGPU is enabled, also use the GPU to accelerate reciprocal space electrostatic interactions. Disabling this can improve performance on less powerful GPUs.
UseGPUForNeighbor
- Type:
Bool
- Default value:
Yes
- Description:
When UseGPU is enabled, also use the GPU to accelerate neighbor searches. Disabling this can improve performance on less powerful GPUs.
UseOpenMP
- Type:
Bool
- Default value:
No
- Description:
Parallelize LAMMPS calculations using OpenMP threading. Requires a LAMMPS library built with the OMP package.
WorkerCommand
- Type:
String
- Default value:
exec lmp
- Description:
The command to execute to run the external worker. The command is executed in a subdirectory of the results directory. The LAMMPS input commands will be passed to the worker on standard input.
LinearizationEnergyForRepulsion
- Type:
Float
- Default value:
3.0
- Unit:
Hartree
- Description:
The Lennard-Jones potential becomes extremely repulsive at short distances. The distance is determined where the potential reaches this threshold, for smaller distances a linear expression is used, reducing the repulsion.
LoadCharges
- Type:
Block
- Description:
Load charges from a file to be used as forcefield charges
File
- Type:
String
- Description:
Name of the (kf) file
Section
- Type:
String
- Default value:
AMSResults
- Description:
Section name of the kf file
Variable
- Type:
String
- Default value:
Charges
- Description:
variable name of the kf file
NeighborListSkin
- Type:
Float
- Default value:
2.5
- Unit:
Angstrom
- Description:
Thickness of the buffer region added to the NonBondedCutoff when building a neighbor list.
NonBondedCutoff
- Type:
Float
- Default value:
15.0
- Unit:
Angstrom
- Description:
Distance beyond which the non-bonded pair interactions (Coulomb and Van der Waals) will be ignored.
The interactions are smoothly damped starting from 0.9*NonBondedCutoff.
Has no effect on the Coulomb term for 3D-periodic systems, as Ewald summation is used.
PairInteractionTapering
- Type:
Multiple Choice
- Default value:
Potential
- Options:
[None, Potential, Force, CHARMM, CHARMM-Force]
- Description:
Select a method for smoothing non-bonded pair interactions in the distance range between 90% and 100% of the [NonBondedCutoff] to avoid energy and force jump near the cutoff.
Potential - use a 7th order polynomial switching function that has zero 1st, 2nd and 3rd derivatives at both ends of the interval (force matches the energy derivative).
Force - the same switching function is applied both to the potential and the force (so the force does not match the energy), which may break the total energy conservation during MD.
CHARMM - use a different polynomial that does not have a decaying 2nd derivative at NonBondedCutoff.
CHARMM-Force - use the same switching function as CHARMM but apply it both to the energy and the forces.
SoftCorePotentials
- Type:
Block
- Description:
When performing free energy perturbation the LJ interactions must be scaled by lambda. To avoid numerical instabilities at small lambda, soft-core potentials need to be used (see DOI:10.1021/ct900587b).
Alpha
- Type:
Float
- Default value:
0.5
- Description:
This parameter determines how far the soft-core potential deviates from the scaled regular LJ potential (at zero the expression is a regular LJ expression).
Enabled
- Type:
Bool
- Default value:
No
- Description:
Set to True to use the scaled soft-core LJ potentials.
Lambda
- Type:
Float
- Default value:
1.0
- Description:
The scaling parameter for the LJ interaction term for free energy perturbation (the window).
TaperPairInteractions
- Type:
Bool
- Default value:
Yes
- Description:
Smooth non-bonded pair interactions in the distance range between 90% and 100% of the [NonBondedCutoff] to avoid energy and force jump near the cutoff. See PairInteractionTapering for more precise tuning.
Type
- Type:
Multiple Choice
- Default value:
UFF
- Options:
[UFF, Amber95, GAFF, Tripos5.2, APPLE&P, UserDefined]
- Description:
Type of force field to be used
UFF
- Type:
Block
- Description:
Option for the UFF force filed.
AtomTypesFile
- Type:
String
- Default value:
mmatomtypes_db
- Description:
Expert option: Select the file that defines how UFF determines the atom types
Database
- Type:
String
- Default value:
general_db
- Description:
Expert option: Select the file that defines the UFF parameters per atom type
ElementsFile
- Type:
String
- Default value:
elements_db
- Description:
Expert option: Select the file that defines the elements known to UFF
Library
- Type:
Multiple Choice
- Default value:
UFF
- Options:
[UFF, UFF4MOF, UFF4MOF-II]
- GUI name:
Force field library
- Description:
Selects the used parameter library.
Verbosity
- Type:
Multiple Choice
- Default value:
Silent
- Options:
[Silent, Normal, Verbose, VeryVerbose]
- Description:
Controls the verbosity of the engine.