4nacl.in

分子动力学模拟程序

#   Sample input file for the MD program, v.>=4.1
#
#   Simulated system consists of 248 flexible SPC water molecules,
#   and 4 Na+Cl- ion pairs
#
#   The specified time scale (60ps after 20ps equilibration) may be not enogh 
#   for obtaining reliable values (this is especially concerns ion-ion RDFs)
#   Only equilibration time for this system is about 100ps
#   
#
#   Lines beginning with "#" are commentaries
#
#   Output controll parameter  
  5              
#   Base file name for output files:
  4nacl
#   Path to the molecular database
  ../moldb
#  Read from        Dump               Check          Zero counter
# restart file?  restart file?         only?          of cpu time?
     .f.               .t.              .f.             .t.
#   NVT ensemble?      NPT ensemble?       Anizotropic NPT?
       .t.                   .f.                .f.
#   Number of molecule types:
   3
#   which molecules:
  H2O  Na+_SD  Cl-_SD
#   Number of molecules:
  248         4          4
#    nonbonded intramolecular interactions:
  .t.           .t.       .t.
#    1 - 4 intramolecular interactions:
  .t.           .t.       .t.    
#   Scaling factor for 1-4 LJ interactions
   1.           1.       1.
#   Scaling factor for 1-4 electrostatic interactions
   1.           1.       1.    
#    intramolecular potential type
  2           0          0
#   temperature(K)     density(g/cm**3)       pressure (atm)
     298.                 1.03                   1.
#   box size (A)                                      Cell
     0.                   0.              0.           0
#  Time step (s)      Small steps in one long
    2.d-15                10
#  Total         Steps for interme-      take averages     dump restart file
#  MD-steps      diate averaging         each .. steps      after .. steps 
  30000               5000                  2                   500
#  T-termostat param(fs)  P-termostat(fs)    NVE+velosity     delta T (K)
#                                             scaling?                   
      30.                    700.               .f.              20.
#  Rcutoff(A)      Rcut-fast forces      check neigbours after .. steps
    0.              5.                       10
#   Ewald parameters:
#   alpha                  fexp
    2.9                    8.8
#   which molecules move:
    .t.        .t.              .t.
#   recalculate list of intramolec. interactions?
    .f.
#  Constrain dynamics?       tolerance parameter   which are constrained?
    .f.                          1.d-4             1  1  1  1  1  1
#  Initial state (from -1 to 4)          zero velocities?
     1                                      .f.
#  Keep initial orientation (0/1)?
     0       0       0        
#  Radius of a hole            Keep initial          Permissible
#  for large molecules         configuration?        deviation?
     10.                           .f.                   3.
#  Change temperature at restart?      Change density?
     .f.                                  .f.
#  Final averaging from ..            XMOL config. file?
     3                                    .f.
#  Cut large forces?         Parameter
    .f.                       1.d-3
#  Calculate RDF?      Dump RDF?     Restart RDF?
    .t.                  .t.           .f.
#  RDF for all sites?     Cutoff-RDF(A)       Resolution
    .f.                    9.5                  190
#  dump trajectory (0/1/2)?    interval(s)      num.of config. in a file
     0                          1.d-14           500
#  dump trajectory of molecules:
     1         1         1
# calculate tcf?   restart tcf?   dump tsf?    NSTEG      JUMP
    .t.            .f.           .t.          200         5
#  which of 12 tcf calculate:
 1 1 1 1 1 1 0 0 0 0 0 0
#   unit vectors for reorientational tcf
  1    1    1
  2    1    1
#  extra parameters  
add 0
#  Number of RDF-s
10            
#   O - O
1  1        
#   O - H 
&2          
1  2        
1  3     
#    O - Na 
1  4       
#    O - Cl
1  5       
#    H - H
&3
2  2
2  3
3  3      
#     H - Na
&2
2  4
3  4        
#     H - Cl
&2
2  5
3  5        
#     Na - Na
4  4         
#     Na - Cl
4  5         
#   Cl - Cl
5  5