[gmx-users] Reading XTC files from fortran90

Sun Sep 30 17:15:08 CEST 2007

Hi Tsjerk.

Thanks for the prompt answer.

Good idea, I can take the atom names from a .gro file, nad, probably some
strange algorithm can also get the number of atoms per molecule and number
of molecules from there, am I right? That would help a lot.

But: I'll still be unable to get atomic masses and point charges. No to
mention the box shape. :( And I'll need a way to read these parameters too,
unless I begin to write all them in a really awfull and strange index file.

>From what I can understand on the "file logistics" of gromacs, these
information are only stored in the whole ".top .itp .atp .rtp structure of
files" or, in a condensed form, in the ".tpr" file. Is that right?

Thanks a lot for all the information and help!

Sincerally yours,

Jones

On 9/30/07, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
>
> Hi Jones,
>
> You probably only need to read the atoms and such from a .pdb or .gro
> file, unless you really want to have topology information (bondedness,
> molecule definitions, etc). Then you do have to read the topology file
> or a .tpr file directly. Don't recall having seen the fortran
> implementations for these... But maybe Bert knows better.
>
> Just one note... There's no shape in PBC. The lattice vectors are all
> there is, and these are stored in the .xtc file (as you already know).
>
> Cheers,
>
> Tsjerk
>
> On 9/30/07, Jones de Andrade <johannesrs at gmail.com> wrote:
> > Hi Bert.
> >
> > Thanks a lot for the help. I've found the mistakes, one programming
> minor
> > issue and a compiler configuration a bit of "hidden" in the config
> files.
> > Old time mistakes just choose to arise at its worst moments. :)
> >
> > At the moment, I already can read the coordinates, number of atoms, box
> > coordinates, step number, simulation time and precision. I guess this is
> all
> > what is stored in the .xtc files themselves, am I right?
> >
> >  I have so one extra question: I guess that extra information as atom
> names,
> > number of molecules of type X, number of molecular types, box and pbc
> > "shape" and atomic charges and masses are *not* stored in the .xtc
> files, am
> > I right? Ok, the "integer" stuff (number of molecules of type X, number
> of
> > molecular types, box and pbc) could be written in a special .ndx file,
> but
> > that would, by all means, looks at least "diselegant".
> >
> > If so, the only two possible ways of getting them is reading or the .top
> and
> > .itp files correctly, or to read the .tpr file, correct? Now, is there
> any
> > guideline available on how to deal with those files?
> >
> > Thanks a lot everybody for all the help.
> >
> >
> > Sincerally yours,
> >
> > Jones
> >
> > On 9/29/07, Bert de Groot <bgroot at gwdg.de> wrote:
> > > On Sat, 29 Sep 2007, Jones de Andrade wrote:
> > >
> > > > Hi Bert.
> > > >
> > > > Thank you for the prompt answer.
> > > >
> > > > Just did as instructed, but got the following:
> > > >
> > > > CruNumMac src/own/B/9/xtc 286% ifort xtciof.f90 test_xtc.f90
> > > > -L/home/johannes/src/own/B/9/xtc/xtc/ -lxrdf -lg2c
> > > > IPO link: can not find -lxrdf
> > >
> > >
> > > well, apparently the path you specify with -L does not contain a
> > > libxdrf.a
> > >
> > > the way you called it the compiler expects it to be located here:
> > > /home/johannes/src/own/B/9/xtc/xtc/libxdrf.a
> > >
> > > also, IIRC, the xtcio stuff is already linked into the libxdrf.a, so
> no
> > > need to include it again.
> > >
> > >
> > > > ifort: error: problem during multi-file optimization compilation
> (code
> > 1)
> > > >
> > > > Looks better, in the sense that the number of error messages was
> > reduced.
> > > > But still doesn't accept to link to the xrdf library.
> > > >
> > > > Tried that with and without re-make of the library (strange fact
> that
> > the
> > > > SGI arch is to be used in linux) and also tried to say -llibxrdf
> instead
> > of
> > > > -lxrdf. Nothing worked.
> > > >
> > > > Have you or someone come across such an error before? Any clue of
> what
> > can
> > > > possibly be going wrong?
> > > >
> > > > Thanks a lot in advance...
> > > >
> > > > Sincerally yours,
> > > >
> > > > Jones
> > > >
> > > > On 9/29/07, Bert de Groot <bgroot at gwdg.de> wrote:
> > > > >
> > > > > Hi,
> > > > >
> > > > > try:
> > > > >
> > > > > download
> > > > > http://www.mpibpc.gwdg.de/groups/de_groot/xtc.tar.gz
> > > > >
> > > > > (and optionally issue a 'make' in the xtc directory after
> unpacking)
> > > > >
> > > > > in the linking stage, use something like
> > > > >
> > > > > ifort -blabla -lxdrf -L/wherever/xtc -lg2c
> > > > >
> > > > > your smalll test code looks OK apart from the fact that I don't
> know
> > what
> > > > > happens if you read&write from the same file.
> > > > >
> > > > > Bert
> > > > >
> > > >
> > >
> > >
> > > Bert
> > >
> > >
> > >
> > > ________________________________________________
> > > Bert de Groot, PhD
> > >
> > > Max Planck Institute for Biophysical Chemistry
> > > Computational biomolecular dynamics group
> > > Am Fassberg 11
> > > 37077 Goettingen, Germany
> > >
> > > tel: +49-551-2012308, fax: +49-551-2012302
> > >
> > > http://www.mpibpc.gwdg.de/groups/de_groot
> > > _______________________________________________
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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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