md.input

分子动力学模拟程序

#   Sample input file for the MD program, v.>=4.3
#
#   Simulated system consists of 246 flexible SPC water molecules,
#   and 5 Na+Cl- ion pairs
#
#   Lines beginning with "#" are commentaries
#   In this file the commentaries go before the corresponding parameters.
#
#   This file can be directly used as input (see directory sample for
#   short version of the input file)
#
#
#   Output control parameter
#   Suitable valus 2-10. The less number, the less you see in the output
#   parameters higher 7 used mostly for debug purposes  
  5                                            
#
#   Base file name for output files:                  
#   Other files requested or created by the program have this name with 
#   various extensions
  5nacl
#
#   Path to the molecular database
#   This directory contains *.mol files wich describe the molecular
#   structure and the force field
  ./moldb  
#                      
# The program creates and updates periodically a restart file which
# contains configuration of the system and calculated averages.
# The program can be interrupted and then continued from the restart file
# without loosing any information.
#  If "Check only" parameter is true, the program does not run
# simulation. If it is a new run, the program only checks the input.
# If it is continuation of the old run, the program gives calculated results.
#  
#  Read from        Dump               Check          Zero counter
# restart file?  restart file?         only?          of cpu time?
     .f.               .t.              .f.             .t. 
#
#  The type of statistical ensemble. "Anizotropic NPT" means separate 
#  pressure/volume controll in each direction. Use this option only if the
#  system is really anizotropic (a piece of DNA, membrane, liquid crystall, 
#  etc). Note, that for "constant pressure"=.t. "constant temperature"
#  must be also .true. (who knows what is NVP ensemble???).
#  Constant temperature?   Constant pressure?    Anizotropic NPT?
       .t.                     .f.                   .f.
#
#   Number of molecule types:
   3
#
#   which molecules:
#  The database directory (specified above) should contain files
#  H2O.mol, Na+.mol,  Cl-.mol    
#  See README file about format of .mol files
  H2O         Na+        Cl-                 
#
#   For each molecule:
#   Number of molecules:
  246         5          5
#
#    non-bonded intramolecular interactions:
#   Calculate intramolecular potential (LJ and electrostatic)
#   for non-bound atoms, separated by
#   more than 3 covalent bonds. Normally, it should be .true. 
#   unimportant for small molecules)
  .t.           .t.       .t.   
#
#    1 - 4 intramolecular interactions:
#   Calculate LJ and electrostatic terms for 1-4 (i.e. separated by
#   3 covalent bonds) intramolecular interactions
  .f.           .f.       .f.    
#   Scaling factors for 1-4 LJ interactions       
#   These are 0 in AMBER, 1 in CHARMM and 0.25 in GROMOS
#   Not important for small molecules
   1.           1.       1.
#   Scaling factor for 1-4 electrostatic interactions
   1.           1.       1.
#    
#    intramolecular potential type   
#    Now it should be 0 for all molecules except the water
#    For water 1 is "harmonic" and 2 "anharmonic" flexible SPC water
#    (It says the program to use a special subroutine)
  2           0          0         
#
#   Rules for initial box size / density:
#    - If one of the box sizes is zero, the actual box size (cubic box) 
#   is defined by the density. 
#    - If the density is also zero, the program run "vaccum 
#   simulations". Set Ewald parameters (below) to 0 in the case of 
#   vaccum simulations.
#    - If all the three box sizes are not zero, they define initial box size
#   and shape, and so the actual density    
#
#   Cell type:
#   0 - rectangular
#   1 - truncated octahedron: cube of side BOXL centred in 0,0,0 with
#           truncated corners:      |x|+|y|+|z| < 0.75*BOXL
#   2 - hexagonal along Z axis   
#
#   temperature(K)     density(g/cm**3)       pressure (atm)
     298.                 1.03                   1.
#   box size (A)                                             cell type
     0.                   0.                    0.               0
#
#  This is the long time step
#  Time step (s)      Small steps in one long
    2.d-15                10
#
# Total (long)   Steps for interme-      take averages     dump restart file
#  MD-steps      diate averaging         each .. steps      after .. steps 
  10000               1000                  1                   500
#
# Nose termostat parameters:                 Meaningful in constant-energy
#                                            simulations (if const.temp.=.f.):
#  T-termostat param(fs)  P-termostat(fs)    Simple velosity   delta T (K)
#                                             scaling?                   
      30.                    700.               .f.              20.
#
#  Rcutoff sets cut off radius for LJ and Real-space electrostatic forces
#  Interaction inside Rcut-fast are recalculated each short time step,
#  interactions between Rcut-fast and Rcutoff each long time step
#  
#  Rcutoff(A)      Rcut-fast forces      check neigbours after .. steps
    10.              5.                       10
#===========================================                          
#   Treatment of electrostatic interactions:
#
#   Ewald parameters:  
#   alpha and fexp are set from the conditions: 
#  erfc(alpha*R)=required precision of the real-space Ewald
#  exp(-fexp)=required precision of reciprocal-space Ewald 
#    the rule of thumb:
#    alpha*R                 fexp (m/s**2)
     3.14159256            9.81             
#   If alpha*R above is negative, the reaction field method is used with
#   -alpha*R as dielectric permitivity, fexp is Debay screening length in