[gmx-developers] force field reorganization done

[Berk Hess]

David van der Spoel wrote:
> On 1/28/10 10:08 AM, Berk Hess wrote:
>> David van der Spoel wrote:
>>> On 1/28/10 9:52 AM, Berk Hess wrote:
>>>> David van der Spoel wrote:
>>>>> Another small thing:
>>>>>
>>>>> pdb2gmx now generates topologies with the full path to the forcefield
>>>>> files, e.g.:
>>>>>
>>>>> ; Include forcefield parameters
>>>>> #include
>>>>> "/home/spoel/software-5.0b/share/gromacs/top/oplsaa.ff/forcefield.itp"
>>>>>
>>>>>
>>>>> Is that what we want?
>>>>> If I remove the path in
>>>>> [anfinsen:water/tip4p] % echo $GMXDATA
>>>>> /home/spoel/software-5.0b/share
>>>>>
>>>>> to get
>>>>> ; Include forcefield parameters
>>>>> #include "gromacs/top/oplsaa.ff/forcefield.itp"
>>>>>
>>>>> grompp does not find the include files anymore.
>>>>>
>>>>> We probably need to update some code in gmxcpp.c to fix it, such that
>>>>> paths relative to $GMXDATA are still recognized.
>>>>>
>>>> I noticed this full path thing as well.
>>>> I can probably fix that in pdb2gmx.
>>>>
>>>> The question is if we always want to
>>>> include<ffname>.ff/forcefield.itp,
>>>> even when you have explicitly set the GMXLIB env var.
>>>> I guess that in that case you do want the full path.
>>>>
>>>> GMXDATA is set but currently not used by any Gromacs program.
>>>> So I think we should currently not rely on that, unless we decide
>>>> to do
>>>> so and check it thoroughly.
>>>>
>>>> Berk
>>>>
>>> It is more a grompp problem, if you write topologies yourself you have
>>> to give the full path to the force field files.
>>>
>> No, when I fix pdb2gmx things will be as before.
>> Or is gmxcpp (and cpp?) not capable of finding files in a subdirectory
>> of the share/top dir?
>> In that case this functionality needs to be implemented in gmxcpp.c.
>>> Maybe we should kick out both GMXDATA and GMXLIB variables, and rely
>>> on the installation information?
>>>
>> Currently GMXDATA is never used and GMXLIB is never set.
>> The GMXLIB functionality is very useful and should stay there, but
>> GMXLIB is not by default.
>> By default all programs locate share/top from the binary location.
>>
>> Berk
>>
> But if I have:
> [anfinsen:water/tip4p] % cat topol.top
> #include "oplsaa.ff/forcefield.itp"
> #include "oplsaa.ff/tip4p.itp"
>
> [ system ]
> 512 TIP/4P
>
> [ molecules ]
> SOL    512
>
> grompp tells me
>
> Program grompp, VERSION 4.0.99_development_20090927
> Source code file: /home/spoel/GG/gromacs/src/gmxlib/gmxcpp.c, line: 232
>
> Fatal error:
> Can not chdir to oplsaa.ff when processing topology. Reason: No such
> file or directory
>
>
> This has nothing to do with pdb2gmx.
>
>
Is this with a completely installed Gromacs system?
The share/top dir location has to be inferred from the path of the binary.
For me it works after a make install and calling pdb2gmx from the
installed directory.

Berk