|
Allowable |
Default |
|
Keyword |
Value |
Value |
Description |
NUMSTEPS |
Int > 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. |
|
Allowable |
Default |
|
Keyword |
Value |
Value |
Description |
TITLE |
any string |
(none) |
Sting 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'' |
Allow (yes) or remove (no) center of mass motion. |
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 |
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 |
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 |
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 |
UNITCELL |
``on'' or ``off'' |
``off'' |
Flag controlling use of periodic boundary conditions. |
UNITORIGIN |
3 floats |
(none) |
Coordinates of the unit cell origin. |
UNITX |
3 floats |
(none) |
End-point coordinates of unit cell X axis. |
UNITY |
3 floats |
(none) |
End-point coordinates of unit cell Y axis. |
UNITZ |
3 floats |
(none) |
End-point coordinates of unit cell Z axis. |
PERIODICITY |
``x'', ``y'', ``z'', ``xy'', ``xz'', ``yz'', ``xyz'' |
``xyz'' |
Cell axes which are periodic. |
|
Allowable |
Default |
|
Keyword |
Value |
Value |
Description |
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
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
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. |