[gmx-users] problem in running gromacs demo

nitu sharma sharmanitu35 at gmail.com
Thu Feb 26 10:53:28 CET 2009


Dear all,

                       I  have successfully installed the gromacs 4.0.3  it
is working but the problem is when I want to run the gromacs demo during
processing when I put the command "grompp -v" the output like this ,:-)  G
R  O  M  A  C  S  (-:

                  Gromacs Runs On Most of All Computer Systems

                            :-)  VERSION 4.0.3  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         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     grompp.mdp  Input, Opt.  grompp input file with MD parameters
 -po      mdout.mdp  Output       grompp input file with MD parameters
  -c       conf.gro  Input        Structure file: gro g96 pdb tpr tpb tpa
  -r       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
 -rb       conf.gro  Input, Opt.  Structure file: gro g96 pdb tpr tpb tpa
  -n      index.ndx  Input, Opt.  Index file
  -p      topol.top  Input        Topology file
 -pp  processed.top  Output, Opt. Topology file
  -o      topol.tpr  Output       Run input file: tpr tpb tpa
  -t       traj.trr  Input, Opt.  Full precision trajectory: trr trj cpt
  -e       ener.edr  Input, Opt.  Energy file: edr ene

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-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.
-[no]rmvsbds bool   yes     Remove constant bonded interactions with virtual
                            sites
-maxwarn     int    0       Number of allowed warnings during input
processing
-[no]zero    bool   no      Set parameters for bonded interactions without
                            defaults to zero instead of generating an error
-[no]renum   bool   yes     Renumber atomtypes and minimize number of
                            atomtypes

Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'domain-decomposition'
Replacing old mdp entry 'unconstrained-start' by 'continuation'
Ignoring obsolete mdp entry 'dihre-tau'
Ignoring obsolete mdp entry 'nstdihreout'
Ignoring obsolete mdp entry 'nstcheckpoint'

WARNING 1 [file grompp.mdp, line unknown]:
  Unknown or double left-hand 'bd-temp' in parameter file


checking input for internal consistency...

NOTE 1 [file grompp.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.

processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxbon.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
Generated 1284 of the 1485 non-bonded parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
renumbering atomtypes...
converting bonded parameters...
initialising group options...
processing index file...
Analysing residue names:
Opening library file /usr/local/gromacs/share/gromacs/top/aminoacids.dat
There are:   216      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
Making dummy/rest group for Acceleration containing 648 elements
Making dummy/rest group for Freeze containing 648 elements
Making dummy/rest group for Energy Mon. containing 648 elements
Making dummy/rest group for VCM containing 648 elements
Number of degrees of freedom in T-Coupling group System is 1293.00
Making dummy/rest group for User1 containing 648 elements
Making dummy/rest group for User2 containing 648 elements
Making dummy/rest group for XTC containing 648 elements
Making dummy/rest group for Or. Res. Fit containing 648 elements
Making dummy/rest group for QMMM containing 648 elements
T-Coupling       has 1 element(s): System
Energy Mon.      has 1 element(s): rest
Acceleration     has 1 element(s): rest
Freeze           has 1 element(s): rest
User1            has 1 element(s): rest
User2            has 1 element(s): rest
VCM              has 1 element(s): rest
XTC              has 1 element(s): rest
Or. Res. Fit     has 1 element(s): rest
QMMM             has 1 element(s): rest
Checking consistency between energy and charge groups...

NOTE 2 [file grompp.mdp, line unknown]:
  You are using a plain Coulomb cut-off, this will often produce artifacts.
  You might want to consider using PME electrostatics.


This run will generate roughly 1 Mb of data
writing run input file...

There were 2 notes

There was 1 warning

-------------------------------------------------------
Program grompp, VERSION 4.0.3
Source code file: gmx_fatal.c, line: 481

Fatal error:
Too many warnings (1), grompp terminated.
If you are sure all warnings are harmless, use the -maxwarn option.
-------------------------------------------------------

"How Do You Like Your Vacation So Far ?" (Speed 2 - Cruise Control) why the
grompp -v terminated  even i am going step by step as in mannual.
could you please anybody tell me about that.
 Thank you very much in advance.

Nitu sharma

Structural Biology lab
Schoolof Life Sciences
Jawaherlal Nehru University
New Delhi,India

 gmxdump -s topol.tpr | more
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