[gmx-users] Re: grompp 4.0.5 hangs while 3.2.1 works

[Kaihsu Tai]

It seems that there was some change in reading the fields 
‘cpp’, ‘include’, and ‘define’ from the .mdp file. Now I 
have set the GMXLIB environment variable rather than relying 
on those .mdp fields and it seems to work. Cheers.

Kaihsu Tai, 2009-05-21 16:07:03+0100:
> I have a system which works with grompp 3.2.1 but grompp 
> 4.0.5 hangs at ‘processing topology...’. Is there 
> something that had changed (say, file format in .top or 
> .itp) that could have caused this? I can supply my 
> topology, conformation, etc. files if necessary for 
> debugging. Cheers.
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[gmx-users] grompp 4.0.5 hangs while 3.2.1 works

[Kaihsu Tai]

I have a system which works with grompp 3.2.1 but grompp 
4.0.5 hangs at ‘processing topology...’. Is there something 
that had changed (say, file format in .top or .itp) that 
could have caused this? I can supply my topology, 
conformation, etc. files if necessary for debugging. Cheers.

$ grompp -v -f test0_.mdp -po test0.mdp -c initial.gro   -p Kir21.top -o 
test0.tpr
 :-)  G  R  O  M  A  C  S  (-:

  GROwing Monsters And Cloning Shrimps

:-)  VERSION 4.0.5  (-:


  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 test0_.mdp  Input, Opt!  grompp input file with MD parameters
 -po  test0.mdp  Output   grompp input file with MD parameters
  -cinitial.gro  InputStructure 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  Kir21.top  InputTopology file
 -pp  processed.top  Output, Opt. Topology file
  -o  test0.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
-niceint0   Set the nicelevel
-[no]v   bool   yes Be loud and noisy
-timereal   -1  Take frame at or first after this time.
-[no]rmvsbds bool   yes Remove constant bonded interactions with virtual
sites
-maxwarn int0   Number of allowed warnings during input processing
-[no]zerobool   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'

Back Off! I just backed up test0.mdp to ./#test0.mdp.7#
checking input for internal consistency...

NOTE 1 [file test0_.mdp, line unknown]:
  The Berendsen thermostat does not generate the correct kinetic energy
  distribution. You might want to consider using the V-rescale thermostat.


ERROR: With coulombtype = PME, rcoulomb must be equal to rlist
If you want optimal energy conservation or exact integration use PME-Switch

processing topology...

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