Keywords

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 envoked 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

ForceFieldPatchFile
Type

String

Default value

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.

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 “$AMSBIN/amspython” “$AMSHOME/scripting/scm/external_engines/lmpworker.py”

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.

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.