[gmx-users] sridhar-problem with cg minimization in gromacs.

Mr.Sridhar sridhar at www.cdfd.org.in
Tue Apr 29 07:52:01 CEST 2003

Dear Mr. David,

Thank you for your reply. I have used flexible water by specifying
-DFLEX_SPC for define and "none" for constraints. I also used nstcgsteep =
1000. but still the grompp command is not working saying that conjugate
gradients cannot be performed with constraints. I dont understand still
what constraints have to be removed.


-------------- next part --------------
                         :-)  G  R  O  M  A  C  S  (-:

        Getting the Right Output Means no Artefacts in Calculating Stuff

                            :-)  VERSION 3.1.4  (-:

       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  (-:

Option     Filename  Type          Description
  -f  emcg_1ptr.mdp  Input, Opt!   grompp input file with MD parameters
 -po b4emcg_1ptr.mdp  Output        grompp input file with MD parameters
  -c  emsd_1ptr.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       1ptr.top  Input         Topology file
 -pp  processed.top  Output, Opt.  Topology file
  -o b4emcg_1ptr.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

creating statusfile for 1 node...

Back Off! I just backed up b4emcg_1ptr.mdp to ./#b4emcg_1ptr.mdp.2#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 135 of the 1081 non-bonded parameter combinations
Excluding 3 bonded neighbours for Protein 1
Excluding 2 bonded neighbours for SOL 2002
Excluding 1 bonded neighbours for CL- 7
processing coordinates...
double-checking input for internal consistency...
ERROR: can not do Conjugate Gradients with constraints (29)
Fatal error: There was 1 error
-------------- next part --------------
;	User swetha
title 		    =  1ptr
cpp                 =  /usr/bin/cpp ; the c pre-processor
define              =  -DFLEX_SPC
constraints         =  none
integrator          =  cg
nsteps              =  15000
nstlist		    =  10
fourierspacing	    =  0.12
fourier_nx	    =  0
fourier_ny	    =  0
fourier_nz	    =  0
pme_order	    =  4
ewald_rtol	    =  1e-5
optimize_fft	    =  yes
coulombtype	    =  PME
;	Energy minimizing stuff
emtol               =  0.1
emstep              =  0.001
nstcgsteep	    =  1000
nstcomm             =  1
ns_type             =  grid
rlist               =  1
rcoulomb            =  1
rvdw                =  1.4
Tcoupl              =  no
Pcoupl              =  no
gen_vel             =  no

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