[gmx-developers] include files / cmake

[David van der Spoel]

Victor Rühle wrote:
> We're developing a package for coarse-graining applications which also 
> uses the gromacs libraries. With molfile_plugin.h missing, compiling 
> against the gromacs installation is not possible, that's why the file 
> should be installed.
> 
> For such a scenario, there is an additional problem with malformated 
> include directives in the gromacs headers (I reported this some time 
> ago), however this can be solved by some unhandy CPPFLAGS even though 
> GROMACS headers are in standard include directory.
> 

This is a good point that I was fighting today. Even though gromacs 
include files are installed in $PREFIX/include/gromacs the include files 
are referred to as
#include "typedefs.h"
although it works fine to compile gromacs this way, for a third party 
package that needs to link to gromacs, this complicates matters (at 
least with cmake). Would it be possible to include all files like 
"gromacs/typedefs.h" ?


> Cheers,
> Victor
> 
> Roland Schulz wrote:
>>
>>
>> On Mon, Nov 30, 2009 at 11:44 AM, Victor Rühle 
>> <ruehle at mpip-mainz.mpg.de <mailto: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 <http://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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>>
>>
>>
>> -- 
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 
>> <http://cmb.ornl.gov>
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>>
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, 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