REQUIRED | BASIC | INPUT FILES | OUTPUT FILES |
TRAJECTORY FILES | CONSTRAINTS | FMA | MINIMIZE |
LANGEVIN | TEMPERATURE | SPHERICAL | ELECTRIC |
Keyword | Allowable Value | Default | Description | Input |
NUMSTEPS | Integer > 0 | (none) | Number of time steps desired. | |
COORDINATES | UNIX file name | (none) | Name of initial coordinates file. | |
OUTPUTNAME | UNIX file name | (none) | .vel and .coord output file prefix. | |
STRUCTURE | UNIX file name | (none) | Name of molecular structure file. | |
PARAMETERS | UNIX file name | (none) | Name of force-field parameter file. More than one file may be used. Last value seen is value used. | |
CUTOFF | Float > 0 | (none) | Local interaction distance. | |
EXCLUDE | ``1-2'', ``1-3'', ``1-4'', ``scaled1-4'', ``none'' | (none) | Specifies pairs of bonded atoms to exclude from non-bonded interactions. |
yes | Processors |
no |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
TITLE | any string | (none) | String to use as title in output and various files. | |
TITLE2 | any string | (none) | Subtitle used as title above. | |
TIMESTEP | Float > 0 | 1.0 | Time step size in femto-seconds. | |
TEMPERATURE | Float >= 0 | (none) | Random initial velocities will be set to satisfy this temperature. One of TEMPERATURE or VELOCITIES must be set. | |
COMMOTION | ``yes'' or ``no'' | ``no'' | Flag removal of center of mass motions. | |
DIELECTRIC | Float >= 1.0 | 1.0 | Dielectric constant for model. | |
1-4SCALING | 0.0 <= Float <= 1.0 | 1.0 | Scaling for 1-4 interactions. | |
CWD | UNIX directory name | (none) | Default working directory. | |
SEED | Int > 0 | (none) | Random number generator seed. | |
OUTPUTENERGIES | Int > 0 | 1 | Time step frequency at with energies are printed to output file. | |
SWITCHING | ``on'' or ``off'' | ``off'' | Flag to determine handling of van der Waals forces at the cutoff. | |
SWITCHDIST | cutoff >= Float >= 0.0 | (none) | Distance at which van der Waals switching function takes effect. | |
PAIRLISTDIST | Float >= cutoff | CUTOFF | Maximum pair separation for inclusion in pair list. | |
STEPSPERCYCLE | Int > 0 | 20 | Number of time steps in a cycle. | |
MARGIN | Float > 0.0 | 1.0 | Patch size tuning parameter. |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
INITCOORDSFILE | UNIX file name | (none) | Specifies initial coordinate set. | |
INITCOORDSFORMAT | ``pdb'', ``bin'' or ``hdf'' | ``pdb'' | Format of the initial coordinates file. | |
INITCOORDSDATASET | Int >= 0 | 0 | Specifies dataset for initial coordinates, if HDF format is being used. | |
VELOCITIES | UNIX file name | (none) | Name of initial velocities file. See TEMPERATURE below. | |
VELOCITIESFORMAT | ``pdb'', ``bin'' or ``hdf'' | ``pdb'' | Format of the initial velocities file. | |
VELOCITIESDATASET | Int >= 0 | 0 | Specifies dataset for initial velocities, if HDF format is being used. |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
OUTPUTFORMAT | ``pdb'', ``bin'' or ``hdf'' | ``pdb'' | Format to use when writing the output files (.coord and .vel). Currently, only ``pdb'' and ``hdf'' are available. | |
RESTARTNAME | UNIX file name | (none) | Prefix for .vel and .coord restart file names. Similar to OUTPUTNAME above, but written more than once. | |
RESTARTFREQ | Int > 0 | (none) | Time step frequency for writing restart files. | |
RESTARTFORMAT | ``pdb'', ``bin'' or ``hdf'' | ``pdb'' | Format to use when writing restart files. Currently only ``pdb'' and ``bin'' are available. |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
DICEFREQ | Int > 0 | 1 | Time step frequency for updating DICE (coordinates, velocities, energies). | |
COORTRJFILE | UNIX file name | (none) | Coordinate trajectory file name. | |
COORTRJFREQ | Int > 0 | (none) | Time step frequency for writing coordinate trajectory data. | |
COORTRJFORMAT | ``dcd'' or ``hdf'' | ``dcd'' | Coordinates trajectory file format. | |
ENERGYTRJFILE | UNIX file name | (none) | Energy trajectory file name (HDF only). | |
ENERGYTRJFREQ | Int > 0 | (none) | Time step frequency for writing energy trajectory data. | |
VELTRJFILE | UNIX file name | (none) | Velocity trajectory file name. | |
VELTRJFREQ | Int > 0 | (none) | Time step frequency for writing velocity trajectory data. | |
VELTRJFORMAT | ``dcd'' or ``hdf'' | ``dcd'' | Velocity trajectory file format. | |
SNAPSHOTFILE | UNIX file name | (none) | Coordinate trajectory file over a specified range of time steps. | |
SNAPSHOTFORMAT | ``dcd'' or ``hdf'' | ``dcd'' | Format of the snapshot trajectory file. | |
SNAPSHOTSTART | Int > 0 | (none) | Snapshot start step. | |
SNAPSHOTSTOP | Int > 0 | (none) | Snapshot end step. |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
FMA | ``off'', ``FMM3D'', ``AndersonNA'', ``AndersonA'' | ``off'' | Select long range force method. | |
FMALEVELS | Int > 0 | 3 | Number of FMM3D tree levels. | |
FMAMP | Int > 0 | 5 | Number of multipole expansion terms. | |
FMADEGSEP | Int >= 0 | 0 | Degree of separation to use in the Anderson methods. | |
FMASUPERNODE | Int > 0 | 0 | Number of super nodes to use in the Anderson methods. |
HARMONIC CONSTRAINTS PARAMETERS
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
CONSTRAINTS | ``on'' or ``off'' | ``off'' | Flag controlling use of harmonic constraints. | |
CONSEXP | Int > 0 and even | 2 | Constraint energy function exponent. | |
CONSREF | UNIX file name | COORDINATES | Coordinate PDB file giving zero point coordinates. Default implies constraint to initial position. | |
CONSKOL | ``X'', ``Y'', ``Z'', ``O'', ``B'' | ``O'' | Column in PDB file with coefficient data. | |
CONSKFILE | UNIX file name | COORDINATES | PDB file containing constraint coefficients. |
ENERGY MINIMIZATION PARAMETERS
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
MINIMIZATION | ``on'' or ``off'' | ``off'' | Flag controlling energy minimization. | |
MAXIMUMMOVE | Float > 0.0 | (0.75 * cuttoff)/(stepspercycle) | Maximum distance any atom can move in a step, units of Å. |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
LANGEVIN | ``on'' or ``off'' | ``off'' | Flag controlling Langevin dynamics. | |
LANGEVINTEMP | Float > 0.0 | (none) | Temperature applied to affected atoms. | |
LANGEVINFILE | UNIX file name | COORDINATES | PDB file containing Langevin parameters. | |
LANGEVINCOL | ``X'', ``Y'', ``Z'', ``O'', ``B'' | ``O'' | Column in PDB file containing coefficient. |
TEMPERATURE RESCALING PARAMETERS
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
RESCALETEMP | Float > 0 | (none) | Desired equilibration temperature. | |
RESCALEFREQ | Int > 0 | (none) | Number of time steps between rescalings. |
SPHERICAL BOUNDARY CONDITION PARAMETERS
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
SPHERICALBC | ``on'' or ``off'' | ``off'' | Flag controlling application of spherical boundary conditions. | |
SPHERICALBCR1 | Float > 0.0 | (none) | Distance from center of mass at which first boundary takes effect, in units of Å. | |
SPHERICALBCK1 | Float NEQ 0.0 | (none) | Coefficient for the first boundary force. | |
SPHERICALBCEXP1 | Int > 0, and even | 2 | Exponent for the the first boundary force. | |
SPHERICALBCR2 | Float > 0.0 | (none) | Distance from center of mass at which second boundary takes effect, in units of Å. | |
SPHERICALBCK2 | Float NEQ 0.0 | (none) | Coefficient for the second boundary force. | |
SPHERICALBCEXP2 | Int > 0, and even | 2 | Exponent for the the second boundary force. | |
SPHERICALBCCENTER | Any three floats | C.O.M. | Fixed center for spheres. |
Allowable | Default | |||
Keyword | Value | Value | Description | Input |
EFIELDON | ``on'' or ``off'' | ``off'' | Flag controlling application of of external electric field. | |
EFIELD | Any three floats | (none) | Applied electric field vector. |