[gmx-users] using fortran for xtc files
Jones de Andrade
johannesrs at gmail.com
Sat Mar 24 21:50:51 CET 2007
Hi David.
I would say the .top files. .tpr are not of interest in this point, extra
and unnecessary information (at least, I expect).
I would prefer this in fortran if possible, cause it would more easy for me
to manage. But I don't expect it exists.
About the gromacs C files involved: which ones should I look at?
Sorry for not making myself clear in the previous message.
Thanks a lot in advance,
Jones
On 3/24/07, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
>
> Jones de Andrade wrote:
> > Hi all!
> >
> > About the "same" subject... Does anybody ever tried to read the topology
> > files from gromacs within fortran?
> top or tpr? The latter is out of the question I'd say.
>
> >
> > I would accept some C routines for this if necessary... :)
>
> these are in the code of course, but you basically have to link to the
> gromacs library.
>
> >
> > Thanks a lot,
> >
> > Jones
> >
> > On 3/24/07, *Tsjerk Wassenaar* <tsjerkw at gmail.com
> > <mailto:tsjerkw at gmail.com>> wrote:
> >
> > Hi Gurpreet,
> >
> > Try to get your hands on the original CONCOORD source code
> > (http://www.mpibpc.gwdg.de/groups/de_groot/concoord/ ; version 1.2
> > will do). It is written in fortran, and includes the routines to
> read
> > and write xtc files.
> >
> > Best,
> >
> > Tsjerk
> >
> > On 3/24/07, singh <singh at biophysik.chemie.uni-dortmund.de
> > <mailto:singh at biophysik.chemie.uni-dortmund.de>> wrote:
> > >
> > >
> > >
> > >
> > > Dear Gromacs users,
> > >
> > >
> > >
> > > I am trying to read and write xtc files in fortran . Firstly, I
> > couldn't
> > > find the file in source directory
> > > $(GMXHOME)/src/gmxlib/testxtcf.f in gromacs-3.3.1 as
> > > mentioned on
> > >
> http://www.gromacs.org/documentation/reference_3.3/online/xtc.html.
> > > Even if i copy the code and compile it using the linker options
> > mentioned on
> > > the page, I get the following error
> > >
> > >
> > >
> > > In file test.f:12
> > >
> > > 10 call readxtc(xd,natoms,step,time,box,x,prec,ret)
> > >
> > > 1
> > >
> > > Warning: Label 10 at (1) defined but not used
> > >
> > > /usr/bin/ld: cannot find -lxtcf
> > >
> > > collect2: ld returned 1 exit status
> > >
> > > make: *** [test] Error 1
> > >
> > >
> > >
> > > Any help is appreciated.
> > >
> > >
> > >
> > > With Regards,
> > >
> > > Gurpreet Singh
> > >
> > >
> > >
> > > -------------------------------------------------
> > >
> > > University of Dortmund
> > > Department of Chemistry
> > > Physical Chemistry I - Biophysical Chemistry
> > > Otto-Hahn Str. 6
> > > D-44227 Dortmund
> > > Germany
> > > Office: C1-06 room 176
> > > Phone: +49 231 755 3916
> > >
> > > Fax: +49 231 755 3901
> > >
> > > -------------------------------------------------
> > >
> > >
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> >
> > --
> > Tsjerk A. Wassenaar, Ph.D.
> > Junior UD (post-doc)
> > Biomolecular NMR, Bijvoet Center
> > Utrecht University
> > Padualaan 8
> > 3584 CH Utrecht
> > The Netherlands
> > P: +31-30-2539931
> > F: +31-30-2537623
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> >
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>
> --
> David.
> ________________________________________________________________________
> David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596, 75124 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
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