$MD group                       (relevant if RUNTYP=MD)                         
This group controls the molecular dynamics trajectory for a                     
collection of quantum mechanical atoms and/or Effective                         
Fragment Potential particles.                                                   
A typical MD simulation starts with an equilibration phase,                     
running long enough to produce a randomized structure and                       
velocity distribution.  Typically equilibration is done                         
with an NVT ensemble, allowing the system to equilibrate to                     
a desired temperature.  A production run restarts with the                      
positions and the velocity and quaternion data from the                         
equilibration run, might use either a NVE or NVT ensemble,                      
and collects radial distribution functions and other                            
Only a few properties are computed from the MD trajectory,                      
apart from correct radial distribution functions.  In                           
particular, the pressures, diffusion constants, and heats                       
of vaporization that appear on the printout (presently only                     
for pure EFP runs) are from a preliminary code, which has                       
not yet been verified.                                                          
If the system contains only EFP particles, it may be placed                     
in a periodic box, according to the minimum image                               
convention.  The optional periodic boundary conditions,                         
along with cut-offs, are given in the $EFRAG input.  See                        
also the $EWALD input group for long-range electrostatic                        
treatment if PBC is used.                                                       
            The first keywords relate to the steps:                             
MDINT  = MD integrator selection.                                               
       = FROG (leapfrog).  This is less accurate, and lacks                     
         the special ensemble stepper option NVTNH.                             
       = VVERLET (velocity Verlet) - default.                                   
DT     = MD time step size, in seconds, default=1.0d-15,                        
         which is a femtosecond.                                                
NVTNH    selects a integrator step appropriate to the                           
         desired ensemble.  This is only implemented for                        
         velocity Verlet.                                                       
       = 0 means use NVE Verlet stepping                                        
       = 1 means use NVT Verlet stepping                                        
       = 2 means use Nose/Hoover chain NVT Verlet stepping                      
         The default is 2 if either NVT option RSTEMP or                        
         RSRAND is chosen, but is 0 otherwise.                                  
NSTEPS = number of MD time steps to be found in this run,                       
TTOTAL = total time elapsed in the previous part of a MD                        
         trajectory which is being restarted (READ=.TRUE.).                     
         The default means this trajectory is a new one, or                     
         perhaps the start of a production phase of the MD.                     
         (default=0.0 seconds)                                                  
                      * * *                                                     
BATHT  = bath temperature, in Kelvin (default=300.0)                            
         This value is used during NVT runs, or if the                          
         MD is initialized to a Maxwell-Boltzmann velocity                      
                      * * *                                                     
        Two options exist to create NVT runs, to bring                          
        the system to a desired bath temperature.                               
        If neither is chosen, the ensemble is NVE:                              
RSTEMP = flag to rescale the temperature.  default=.FALSE.                      
DTEMP  = temperature range for the RSTEMP option.  The                          
         velocities are rescaled to the bath temperature                        
         if T < (BATHT-DTEMP) or T > (BATHT+DTEMP).                             
         The default is DTEMP=100.0 degrees.                                    
RSRAND = flag to reset to Maxwell-Boltzmann distribution,                       
         using random numbers (same algorithm as MBT and                        
         MBR) to choose individual velocity magnitudes and                      
         directions.  default=.FALSE.                                           
NRAND  = number of steps for the RSRAND option.  Reassign                       
         velocities (translational and rotational) every                        
         NRAND time steps.  Default=1000.                                       
NVTOFF = step number at which to turn off either NVT                            
         thermostat, and switch to NVE.  At this point, the                     
         NVTNH parameter will be reset to 0, and the PROD                       
         flag will be turned on, so that the production                         
         run will start (gathering and printing the RDF                         
         information to .log file).  This keyword is also                       
         useful in NVE runs to postpone the accumulation of                     
         production information.  The default means no                          
         switch to NVE (default=0).                                             
JEVERY = report simulation quantities (write info such as                       
         energies, temps, etc. to .log file) and collect                        
         RDF info each JEVERY time step.  Default=10                            
KEVERY = write coordinates (to log and TRAJECT files),                          
         velocity/quaternion restart info (to the TRAJECT                       
         file and RDFs (to log file) at each KEVERY step.                       
PROD   = production run, at present this means only that                        
         information for radial distribution functions is                       
         collected, and printed.  default=.FALSE.                               
DELR   = spacing for radial bins in RDF calculations,                           
         default=0.02 Angstroms.                                                
NPROP  = step number at which to begin collecting data for                      
         the other properties, such as pressure and                             
         diffusion constants.  This should be a value                           
         between 1 and NSTEPS, as it counts off the current                     
         run's steps.  Default=0.                                               
PBCOUT = print PBC coordinates in the end of simulation                         
         (i.e. all molecules will be contained in one box)                      
                         * * *                                                  
SSBP   = flag to add spherical solvent boundary condition                       
         using the harmonic restraint potential(V)                              
SFORCE = the force constant for SSBP in kcal/mol-A**2                           
         (default: 0.0).                                                        
CCMS   = flag to add a harmonic potential to constrain                          
         the center of mass of the QM subsystem. This will                      
         keep the QM subsystem in QM/MM-MD with spherical                       
         boundary conditions near the center of sphere.                         
CFORCE = the force constant for CCMS in kcal/mol-A**2                           
         (default: 0.0).                                                        
DROFF  = is an array of distances such that V=0 if R

generated on 7/7/2017