[gmx-users] equilibrating a solvent

Sidney Elmer sidnasty at stanford.edu
Tue Jun 18 00:52:23 CEST 2002

I would appreciate any help anyone could give me on equilibrating a
carbon tetrachloride solvent I made.  I've created the topology file and
the .gro file, now I want to equilibrate it in an NVT ensemble.  What
I've done is written a script that will create a
crystal of the solvent.  I have checked to make sure that I've placed
the necessary number of molecules in the box of a given volume to give
the desired experimental density.  Now I just have to equilibrate the
liquid.  In the .mdp file, whether I specify to use md with Berendson
temperature coupling or stochastic dynamics, I get the same error
message from grompp, which
I have attached to this email.  There are 2560 atoms in the system, but
for some reason, it appears that not all of the atoms are coupled to the

heat bath.  As a side note, I noticed the first time I ran grompp, the
error message specified that it was "Making dummy/rest group for
T-Coupling containing 2555 elements" instead of the 2560.  That is why
I'm thinking that some of the atoms aren't being coupled to the
temperature bath, (but it may be unrelated).  I just don't understand
the Fatal error:  Not enough ref_t and tau_t values.  I will also
include the .mdp file for you as well.  I won't bother sending the .gro
file, because it's pretty big, and it's sufficient to know that there
are 2560 atoms in the file, and the box size is correct on the last
line.  If you could help me I'd appreciate it.  Thanks.

-------------- next part --------------
title                    = Yo
cpp                      = /lib/cpp
define                   = 
integrator               = sd 
dt                       = 0.002
nsteps                   = 1000000
nstxout                  = 1000
nstvout                  = 1000
nstlog                   = 1000
nstenergy                = 1000
bd_temp                  = 300
bd_fric                  = 1
ld_seed                  = 19
energygrps               = CCL4
nstlist                  = 10
ns_type                  = grid 
rlist                    = 0.8
coulombtype              = cut-off
rcoulomb                 = 2.0
rvdw                     = 1.6
;tcoupl                   = Berendsen
;tc-grps                  = CCL4
;tau_t                    = 0.1
;ref_t                    = 300
;Pcoupl                   = Berendsen
;tau_p                    = 1.0
;compressibility          = 4.5e-5
;ref_p                    = 1.0
gen_vel                  = yes
gen_temp                 = 300
gen_seed                 = 173529
constraints              = all-bonds
pbc                      = xyz
-------------- next part --------------
Option     Filename  Type          Description
  -f         md.mdp  Input, Opt!   grompp input file with MD parameters
 -po      mdout.mdp  Output        grompp input file with MD parameters
  -c        out.gro  Input         Generic structure: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.   Generic structure: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt!   Index file
-deshuf  deshuf.ndx  Output, Opt.  Index file
  -p   ccl4_512.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o   ccl4_512.tpr  Output        Generic run input: tpr tpb tpa
  -t       traj.trr  Input, Opt.   Full precision trajectory: trr trj

      Option   Type  Value  Description
      -[no]h   bool     no  Print help info and quit
      -[no]X   bool     no  Use dialog box GUI to edit command line options
       -nice    int      0  Set the nicelevel
      -[no]v   bool    yes  Be loud and noisy
       -time   real     -1  Take frame at or first after this time.
         -np    int      1  Generate statusfile for # nodes
-[no]shuffle   bool     no  Shuffle molecules over nodes
   -[no]sort   bool     no  Sort molecules according to X coordinate
-[no]rmdumbds  bool    yes  Remove constant bonded interactions with dummies
       -load string         Releative load capacity of each node on a parallel
                            machine. Be sure to use quotes around the string,
                            which should contain a number for each node
    -maxwarn    int     10  Number of warnings after which input processing
-[no]check14   bool     no  Remove 1-4 interactions without Van der Waals

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
Generated 135 of the 1081 non-bonded parameter combinations
Excluding 2 bonded neighbours for CCL4             512
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Making dummy/rest group for T-Coupling containing 2560 elements
Fatal error: Not enough ref_t and tau_t values!
                         :-)  G  R  O  M  A  C  S  (-:

             Gallium Rubidium Oxygen Manganese Argon Carbon Silicon

                            :-)  VERSION 3.1.3  (-:

       Copyright (c) 1991-2002, University of Groningen, The Netherlands
         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                                :-)  grompp  (-:

creating statusfile for 1 node...
calling /lib/cpp...
processing topology...
turning all bonds into constraints...
#     ANGLES:   12288
#     CONSTR:   6144

More information about the gromacs.org_gmx-users mailing list