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

[Roland Schulz]

On Mon, Nov 30, 2009 at 12:26 PM, Victor Rühle <ruehle at mpip-mainz.mpg.de>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.
>

Yes. You are absolute right. Sorry. I just fixed it in GIT.


> 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.
>

I don't remember that.

Roland

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
>
>
>
>    --    gmx-developers mailing list
>    gmx-developers at gromacs.org <mailto:gmx-developers at gromacs.org>
>
>    http://lists.gromacs.org/mailman/listinfo/gmx-developers
>    Please don't post (un)subscribe requests to the list. Use the www
>    interface or send it to gmx-developers-request at gromacs.org
>    <mailto:gmx-developers-request at gromacs.org>.
>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov <http://cmb.ornl.gov>
>
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
>
-- 
gmx-developers mailing list
gmx-developers at gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-developers
Please don't post (un)subscribe requests to the list. Use the www interface
or send it to gmx-developers-request at gromacs.org.



-- 
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-developers/attachments/20091130/54148dac/attachment.html>