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

Victor Rühle ruehle at mpip-mainz.mpg.de
Mon Nov 30 17:44:06 CET 2009

Ah, ok thx.

Then I will do my own workaround since I do not need most of the 
additional molecule information (and molecule names could be set later 
on if not present).

Just a last question for that:
What is the best way to detect whether the additional molecule data was 
present in the tpr and read in properly. Is it ok to check if 
mtop.mols.nr and numbers from molblock match, if not only use 
information from mtop.mols? Or is there a better solution?


p.s.: in the dev branch, the file molfile_plugin.h is not copied during 

Berk Hess wrote:
> We can't do that, since these numbers have to match the contents of the
> moltype entry.
> Berk
> 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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