[gmx-users] Trouble with g_disre and 'old' trajectory

Marc Baaden baaden at smplinux.de
Fri Aug 16 12:06:58 CEST 2002


I am trying to verify some things from data that a colleague of mine
did a while ago. Now so far everything went fine. The main problem is
that I had to re-create a tpr file, as I cannot read the one he used
on any of our current machines.

All analysis so far was ok, but checking the distance restraints (which
he had to use) leads to non-sense output like

Index:      0      1      2      3      4      5
Viol:     inf    inf    inf    inf    inf    inf

whereas I could find some former analysis of my colleague, which was fine
with respect to the values he got and the graphs he obtained. For ex.:

Index:     -1     -1     -1     -1     -1     -1
Viol:   0.000  0.000  0.000  0.000  0.000  0.000
Viol:   0.016  0.000  0.000  0.000  0.000  0.000

Now looking at the header of the g_disre output, there is a difference.
In the current output I get 

CPU=  0, lastcg=24114, targetcg=12057, myshift=    0

whereas my colleague got

CPU=  0, lastcg=24116, targetcg=12058, myshift=    0

I wonder whether that could be the origin of the problem. I tried to do
it with the current gromacs version, but also checked with gmx2.0 (which
was what my colleague used), but get the same problem in both cases.

My bet would be that something in the topology is different, but what
could that be ? (I used my colleagues mdp file to re-create the tpr,
as I can't read his for whatever reason)

Any hints appreciated ..


 Dr. Marc Baaden - Laboratory of Molecular Biophysics, Oxford University
 mailto:baaden at smplinux.de  - ICQ# 11466242 -  http://www.marc-baaden.de
 FAX/Voice +49 697912 39550  -  Tel: +44 1865 275380  or  +33 609 843217

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