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FMD User Input Quick Reference 
For FMD Release 1.11.5, dated 17 March 2000


KEYWORD GROUPS  
REQUIRED BASIC INPUT FILES OUTPUT FILES
TRAJECTORY FILES CONSTRAINTS FMA MINIMIZE
LANGEVIN TEMPERATURE PERIODIC SPHERICAL
ELECTRIC      


REQUIRED PARAMETERS 
  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.
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BASIC OPTIONAL PARAMETERS 
  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.
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INPUT FILES 
  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.
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OUTPUT FILES 
  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.
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TRAJECTORY FILES 
  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.
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FMA PARAMETERS 
  Allowable Default  
Keyword Value Value Description
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.
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HARMONIC CONSTRAINTS PARAMETERS 
  Allowable Default  
Keyword Value Value Description
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.
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ENERGY MINIMIZATION PARAMETERS 
  Allowable Default  
Keyword Value Value Description
MINIMIZATION ``on'' or ``off'' ``off'' Flag controlling energy minimization.
MAXIMUMMOVE Float > 0.0 $\frac{0.75 * cuttoff}{stepspercycle}$ Maximum distance any atom can move in a step, units of Å.
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LANGEVIN DYNAMICS PARAMETERS 
  Allowable Default  
Keyword Value Value Description
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.
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TEMPERATURE RESCALING PARAMETERS 
  Allowable Default  
Keyword Value Value Description
RESCALETEMP Float > 0 (none) Desired equilibration temperature.
RESCALEFREQ Int > 0 (none) Number of time steps between rescalings.
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PERIODIC BOUNDARY CONDITION PARAMETERS 
  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.
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SPHERICAL BOUNDARY CONDITION PARAMETERS 
  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 $\neq$ 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.
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ELECTRIC FIELD PARAMETERS 
  Allowable Default  
Keyword Value Value Description
EFIELDON ``on'' or ``off'' ``off'' Flag controlling application of of external electric field.
EFIELD Any three floats (none) Applied electric field vector.
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Next: About this document ...
James A. Lupo
2000-03-20