Hi David.<br><br>I would say the .top files. .tpr are not of interest in this point, extra and unnecessary information (at least, I expect).<br><br>I would prefer this in fortran if possible, cause it would more easy for me to manage. But I don't expect it exists.
<br><br>About the gromacs C files involved: which ones should I look at?<br><br>Sorry for not making myself clear in the previous message.<br><br>Thanks a lot in advance,<br><br>Jones<br><br><div><span class="gmail_quote">
On 3/24/07, <b class="gmail_sendername">David van der Spoel</b> <<a href="mailto:spoel@xray.bmc.uu.se">spoel@xray.bmc.uu.se</a>> wrote:</span><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Jones de Andrade wrote:<br>> Hi all!<br>><br>> About the "same" subject... Does anybody ever tried to read the topology<br>> files from gromacs within fortran?<br>top or tpr? The latter is out of the question I'd say.
<br><br>><br>> I would accept some C routines for this if necessary... :)<br><br>these are in the code of course, but you basically have to link to the<br>gromacs library.<br><br>><br>> Thanks a lot,<br>><br>
> Jones<br>><br>> On 3/24/07, *Tsjerk Wassenaar* <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a><br>> <mailto:<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>>> wrote:<br>><br>
> Hi Gurpreet,<br>><br>> Try to get your hands on the original CONCOORD source code<br>> (<a href="http://www.mpibpc.gwdg.de/groups/de_groot/concoord/">http://www.mpibpc.gwdg.de/groups/de_groot/concoord/
</a> ; version 1.2<br>> will do). It is written in fortran, and includes the routines to read<br>> and write xtc files.<br>><br>> Best,<br>><br>> Tsjerk<br>><br>> On 3/24/07, singh <
<a href="mailto:singh@biophysik.chemie.uni-dortmund.de">singh@biophysik.chemie.uni-dortmund.de</a><br>> <mailto:<a href="mailto:singh@biophysik.chemie.uni-dortmund.de">singh@biophysik.chemie.uni-dortmund.de</a>>> wrote:
<br>> ><br>> ><br>> ><br>> ><br>> > Dear Gromacs users,<br>> ><br>> ><br>> ><br>> > I am trying to read and write xtc files in fortran . Firstly, I
<br>> couldn't<br>> > find the file in source directory<br>> > $(GMXHOME)/src/gmxlib/testxtcf.f in gromacs-3.3.1 as<br>> > mentioned on<br>> > <a href="http://www.gromacs.org/documentation/reference_3.3/online/xtc.html">
http://www.gromacs.org/documentation/reference_3.3/online/xtc.html</a>.<br>> > Even if i copy the code and compile it using the linker options<br>> mentioned on<br>> > the page, I get the following error
<br>> ><br>> ><br>> ><br>> > In file test.f:12<br>> ><br>> > 10 call readxtc(xd,natoms,step,time,box,x,prec,ret)<br>> ><br>> > 1<br>
> ><br>> > Warning: Label 10 at (1) defined but not used<br>> ><br>> > /usr/bin/ld: cannot find -lxtcf<br>> ><br>> > collect2: ld returned 1 exit status<br>
> ><br>> > make: *** [test] Error 1<br>> ><br>> ><br>> ><br>> > Any help is appreciated.<br>> ><br>> ><br>> ><br>> > With Regards,
<br>> ><br>> > Gurpreet Singh<br>> ><br>> ><br>> ><br>> > -------------------------------------------------<br>> ><br>> > University of Dortmund
<br>> > Department of Chemistry<br>> > Physical Chemistry I - Biophysical Chemistry<br>> > Otto-Hahn Str. 6<br>> > D-44227 Dortmund<br>> > Germany<br>> > Office: C1-06 room 176
<br>> > Phone: +49 231 755 3916<br>> ><br>> > Fax: +49 231 755 3901<br>> ><br>> > -------------------------------------------------<br>> ><br>> >
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<br>> Tsjerk A. Wassenaar, Ph.D.<br>> Junior UD (post-doc)<br>> Biomolecular NMR, Bijvoet Center<br>> Utrecht University<br>> Padualaan 8<br>> 3584 CH Utrecht<br>> The Netherlands
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<br>David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,<br>Dept. of Cell and Molecular Biology, Uppsala University.<br>Husargatan 3, Box 596, 75124 Uppsala, Sweden<br>phone: 46 18 471 4205 fax: 46 18 511 755
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