[gmx-developers] force field reorganization done

[David van der Spoel]

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.


-- 
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se