[gmx-users] maximum number of molecules

Rainer Boeckmann rboeckm at gwdg.de
Thu Apr 18 15:45:18 CEST 2002

David van der Spoel wrote:

> On Thu, 18 Apr 2002, Rainer Boeckmann wrote:
> >Hi,
> >
> >a few weeks ago there was a question concerning the maximum number of atoms
> >allowed in GROMACS (2^31-1). I now realized that the maximum number of molecules
> >is limited to about 100.000 - not in mdrun but one gets problems in preparing
> >large systems using editconf. editconf may write wrong coordinates and/or
> >velocities when converting files.
> No it works. Just try it. The largest runs in gromacs we have done here
> are 450,000 atoms.

hmm...not in my case. editconf writes wrong coordinates when for example converting
a g96-file into a pdb-file. In contrast it writes correctly a g96-file from the tpr.
grompp does wrong when writing a tpr-file from a g96, correct when using a pdb-file.
I think that this depends on the number of molecules (more than 100,000 in my case),
not on the number of atoms and appears only when converting a g96-file, but I tested
not all combinations...


Rainer Böckmann
Theoretical Molecular Biophysics Group
Max-Planck-Institute for Biophysical Chemistry
Am Faßberg 11
D-37077 Göttingen

Tel.: +49(551)201-1141, Fax.: +49(551)201-1089
email: rboeckm at gwdg.de

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