<br><br><div class="gmail_quote">On Mon, Nov 30, 2009 at 12:26 PM, Victor Rühle <span dir="ltr"><<a href="mailto:ruehle@mpip-mainz.mpg.de">ruehle@mpip-mainz.mpg.de</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
</blockquote><div>Yes. You are absolute right. Sorry. I just fixed it in GIT.<br> <br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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.<br>
</blockquote><div><br>I don't remember that. <br><br>Roland<br>
<br>
Roland Schulz wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><div></div><div class="h5">
<br>
<br>
On Mon, Nov 30, 2009 at 11:44 AM, Victor Rühle <<a href="mailto:ruehle@mpip-mainz.mpg.de" target="_blank">ruehle@mpip-mainz.mpg.de</a> <mailto:<a href="mailto:ruehle@mpip-mainz.mpg.de" target="_blank">ruehle@mpip-mainz.mpg.de</a>>> wrote:<br>
<br>
<br>
p.s.: in the dev branch, the file molfile_plugin.h is not copied<br>
during installation<br>
<br>
<br>
why does this matter?<br>
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.<br>
<br>
Roland<br>
<br>
<br>
<br>
Berk Hess wrote:<br>
<br>
We can't do that, since these numbers have to match the contents<br>
of the<br>
moltype entry.<br>
<br>
Berk<br>
<br>
Victor Rühle wrote:<br>
<br>
Hi Berk,<br>
<br>
thanks for the quick answer. The only thing I don't<br>
understand then is<br>
the t_block structure mtop.mols which contains at least the<br>
correct<br>
partitioning of atoms into molecules (also in the old tpr<br>
files).<br>
<br>
Since this data is there, wouldn't it be better to<br>
initialize the<br>
mtop.nmolblock.natoms_mol + mtop.nmolblock.nmol accordingly?<br>
<br>
Victor<br>
<br>
Berk Hess wrote:<br>
<br>
Hi,<br>
<br>
The old tpr files do not contain information on<br>
molecular topologies,<br>
so the only thing we can do is consider the whole system<br>
as one large<br>
moleculetype.<br>
<br>
Berk<br>
<br>
Victor Rühle wrote:<br>
<br>
Dear all,<br>
<br>
I changed my code for reading .tpr files to read_tpx<br>
to get molecule<br>
names. When I use the tpr-file generated by a recent<br>
gromacs version,<br>
everything works fine.<br>
<br>
However when using older .tpr files (before molecule<br>
names were<br>
stored), there is an inconsistency in the structures:<br>
<br>
mtop.nmolblock = 1<br>
mtop.nmoltype = 1<br>
<br>
mtop.molblock[0].nmol = 1<br></div></div>
<a href="http://mtop.mols.nr" target="_blank">mtop.mols.nr</a> <<a href="http://mtop.mols.nr" target="_blank">http://mtop.mols.nr</a>> = real number of<div class="im"><br>
molecules<br>
<br>
Is this a bug or a feature? As one can see, at least<br>
some molecule<br>
information is still there but just the new<br>
structures are not set up<br>
properly. If I run tpbconv, it puts all atoms in a<br>
single molecule.<br>
<br>
Possible workarounds are to rerun grompp to create<br>
new tpr files or<br>
change my read function to compensate for this<br>
problem. Both solutions<br>
are not very nice.<br>
<br>
Did anybody else had a similar problem?<br>
<br>
Thanks for your help,<br>
Victor<br>
<br>
<br>
<br>
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