Keywords¶
Links to manual entries¶
Summary of all keywords¶
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
a.u.
- 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 ingore 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 overriden 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 periodic systems, as Ewald summation is used.
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.
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.