[gmx-users] "Gromacs 4 grompp -v" err

li bai javacfish at yahoo.com.cn
Tue Mar 10 10:32:39 CET 2009


Hello,everyone!
Sorry for the last letter!
I have install gromacs4, but when I stury the tutor of gromacs, and input command "grompp -v in every examples", the err be engenderred as below:

li at localhost water]$  grompp -v
                         :-)  G  R  O  M  A  C  S  (-:

               Go Rough, Oppose Many Angry Chinese Serial killers

                            :-)  VERSION 4.0.4  (-:


      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'

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2#

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 /home/bai/workdir/gromacs4/share/gromacs/top/ffgmx.itp
Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ffgmxnb.itp
Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ffgmxbon.itp
Opening library file /home/bai/workdir/gromacs4/share/gromacs/top/ff_dum.itp
Opening library file /home/bai/workdir/gromacs4/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 /home/bai/workdir/gromacs4/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, which might 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 4.0.4
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.
-------------------------------------------------------


Who can help me to solve this problem?


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