ForceField Engine Options¶

Details of the ForceField engine can be set via its input block. Some option are specific to UFF and others to other force fields.

Common options¶

These options apply to any force field.

Type¶

There are a few predefined force field types, that, if used, require no other input.

Type [UFF | Amber95 | GAFF | Tripos5.2 | APPLE&P | UserDefined]

Type
Type: Multiple Choice UFF [UFF, Amber95, GAFF, Tripos5.2, APPLE&P, UserDefined] Type of force field to be used

Non-bonded screening¶

The long range interaction (dispersion and Coulomb) are the most expensive to evaluate. This gives you the option to screen the interaction more aggressively.

NonBondedCutoff float

NonBondedCutoff
Type: Float 15.0 Angstrom 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 periodic systems, as Ewald summation is used.

It is usually a good idea to add some “skin” to the cutoff above when it’s used for computing a neighbor list for changing geometries (e.g. during molecular dynamics or geometry optimization). This way, the neighbor list will not need to be re-computed when atoms move a little. This may save some time because generating a neighbor list can be quite costly. The following option sets the thickness of the “skin”:

NeighborListSkin float

NeighborListSkin
Type: Float 2.5 Angstrom Thickness of the buffer region added to the NonBondedCutoff when building a neighbor list.

Note

This option also affects the cutoff used when generating a neighbor list in the real-space part of the Ewald summation but then it is added to the cutoff radius is used there.

Feedback¶

If you want to know more about the details of the force field you should crank up the verbosity.

Verbosity [Silent | Normal | Verbose | VeryVerbose]

Verbosity
Type: Multiple Choice Silent [Silent, Normal, Verbose, VeryVerbose] Controls the verbosity of the engine.

Bonds usage¶

Bonds can be specified in the input, still you may not want to use those. Here are some options to control this.

BondsUsage [Input | None | Guess | Auto]

BondsUsage
Type: Multiple Choice Auto [Input, None, Guess, Auto] 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.

Ewald summation¶

For periodic systems the Ewald summation is performed for the Coulomb interaction. It has a couple of options:

EwaldSummation
Alpha float
Enabled Yes/No
GridSpacing float
RealSpaceCutoff float
Tolerance float
End

EwaldSummation
Type: Block Configures the details of the particle mesh Ewald (PME) summation of the Coulomb interaction.
Alpha
Type: Float -1.0 1/Angstrom 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 Yes 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 0.5 Angstrom 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 0.0 Angstrom 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 1e-10 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.

Disabling energy terms¶

By default all force field energy terms are calculated, however, you can disable each one of them individually.

EnergyTerms
Angle Yes/No
Coulomb Yes/No
Dispersion Yes/No
Inversion Yes/No
Stretch Yes/No
Torsion Yes/No
End

EnergyTerms
Type: Block expert key, that allows you to disable specific energy terms.
Angle
Type: Bool Yes Whether to use angle (bend) energy.
Coulomb
Type: Bool Yes Whether to use coulomb energy.
Dispersion
Type: Bool Yes Whether to use dispersion energy.
Inversion
Type: Bool Yes Whether to use inversion energy.
Stretch
Type: Bool Yes Whether to use stretch energy.
Torsion
Type: Bool Yes Whether to use torsion energy.

The UFF forcefield has some very rudimentary partial charges guessing, only setting charges for atoms in water molecules. By default the partial charges in a force field calculation are zero. Essentially you will always need to specify atomic charges to make the results more realistic, either via the input or using one or the following options.

GuessCharges¶

The simplest way is the use the GuessCharges key, that uses an engine that can calculate atomic charges. By default DFTB is used. DFTB is of course much more expensive than a forcefield, but if you run a MD calculation you can maybe afford a single DFTB calculation on the system.

GuessCharges Yes/No

GuessCharges
Type: Bool No Use another engine to calculate/guess the charges to be used by the force field.

If you want to control the engine use the GuessChargesConfig key.

GuessChargesConfig
EngineType string
End

GuessChargesConfig
Type: Block Guess charges to be used by the forcefield
EngineType
Type: String dftb Engine that can calculate or guess charges

You have more control over the charge guessing, by loading the charges of another calculation. This way you can set any engine specific detail, such as the basis set, or functional.

You can load charges form a previous calculation to be used as force field charges.

LoadCharges
File string
Section string
Variable string
End

LoadCharges
Type: Block Load charges from a file to be used as forcefield charges
File
Type: String Name of the (kf) file
Section
Type: String AMSResults Section name of the kf file
Variable
Type: String Charges variable name of the kf file

Amber force field options¶

These options are relevant for the Amber and GAFF force fields:

AllowMissingParameters Yes/No

AllowMissingParameters
Type: Bool No When parameters are not found for bonds, angles, dihedrals, or inversions, the first entry in the database will be used.
CheckDuplicateRules Yes/No

CheckDuplicateRules
Type: Bool Yes 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.
ForceFieldFile string

ForceFieldFile
Type: String Force field library Path to the force field parameter file

UFF options¶

The following options are only relevant for the UFF force field:

UFF
AtomTypesFile string
Database string
ElementsFile string
Library [UFF | UFF4MOF | UFF4MOF-II]
End

UFF
Type: Block Option for the UFF force filed.
AtomTypesFile
Type: String mmatomtypes_db Expert option: Select the file that defines how UFF determines the atom types
Database
Type: String general_db Expert option: Select the file that defines the UFF parameters per atom type
ElementsFile
Type: String elements_db Expert option: Select the file that defines the elements known to UFF
Library
Type: Multiple Choice UFF [UFF, UFF4MOF, UFF4MOF-II] Force field library Selects the used parameter library.

APPLE&P force field options¶

The ForceFieldFile key is mandatory and it should contain path to the APPLE&P forcefield file. This file is usually tailored for each system specifically.

Additionally, the following options are relevant for the APPLE&P force field.

DipoleConvergenceThreshold float

DipoleConvergenceThreshold
Type: Float 1e-06 a.u. 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.

The repulsion/dispersion and Coulomb interaction between atoms connected by a bond or by a valence angle are excluded in APPLE&P. Those between atoms connected by a dihedral (the so called 1-4 neighbors) may be scaled down and the scaling factors can be changed using the following options:

APPLE&P
LongRangeCorrection Yes/No
MuMu14Scaling float
QMu14Scaling float
QQ14Scaling float
RD14Scaling float
End

APPLE&P
Type: Block Options for the APPLE&P force field.
LongRangeCorrection
Type: Bool Yes Add long-range correction 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 1.0 Mu-Mu 3rd-neighbor scaling Scaling factor for dipole-dipole interactions between atoms connected to 3rd order (via a dihedral).
QMu14Scaling
Type: Float 0.8 Q-Mu 3rd-neighbor scaling Scaling factor for charge-dipole interactions between atoms connected to 3rd order (via a dihedral).
QQ14Scaling
Type: Float 0.8 Q-Q 3rd-neighbor scaling Scaling factor for charge-charge interactions between atoms connected to 3rd order (via a dihedral).
RD14Scaling
Type: Float 1.0 RD 3rd-neighbor scaling Scaling factor for repulsion/dispersion interactions between atoms connected to 3rd order (via a dihedral).