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

Berk Hess hess at cbr.su.se
Mon Nov 30 17:25:41 CET 2009

We can't do that, since these numbers have to match the contents of the
moltype entry.


Victor Rühle wrote:
> Hi Berk,
> thanks for the quick answer. The only thing I don't understand then is
> the t_block structure mtop.mols which contains at least the correct
> partitioning of atoms into molecules (also in the old tpr files).
> Since this data is there, wouldn't it be better to initialize the
> mtop.nmolblock.natoms_mol + mtop.nmolblock.nmol accordingly?
> Victor
> Berk Hess wrote:
>> Hi,
>> 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
>> moleculetype.
>> Berk
>> 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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