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.