[gmx-developers] gmx_mtop_t inconsistency with old .tpr files

Berk Hess hess at cbr.su.se
Mon Nov 30 16:18:58 CET 2009


The old tpr files do not  contain information on molecular topologies,
so the only thing we can do is consider the whole system as one large


Victor Rühle wrote:
> Dear all,
> I changed my code for reading .tpr files to read_tpx to get molecule
> names. When I use the tpr-file generated by a recent gromacs version,
> everything works fine.
> However when using older .tpr files (before molecule names were
> stored), there is an inconsistency in the structures:
> mtop.nmolblock = 1
> mtop.nmoltype = 1
> mtop.molblock[0].nmol = 1
> mtop.mols.nr = real number of molecules
> Is this a bug or a feature? As one can see, at least some molecule
> information is still there but just the new structures are not set up
> properly. If I run tpbconv, it puts all atoms in a single molecule.
> Possible workarounds are to rerun grompp to create new tpr files or
> change my read function to compensate for this problem. Both solutions
> are not very nice.
> Did anybody else had a similar problem?
> Thanks for your help,
> Victor

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