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

[Roland Schulz]

On Mon, Nov 30, 2009 at 11:44 AM, Victor Rühle <ruehle at mpip-mainz.mpg.de>wrote:

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


why does this matter?
This file is a VMD include file and only included in the GROMACS source to
avoid a dependency on VMD at compile time. But it is not an external
interface to GROMACS. So I don't know why anyone would need that include
file.

Roland


>
>
> 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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