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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> 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 > > > _______________________________________________ > > > gmx-users mailing list gmx-users@gromacs.org > > > http://www.gromacs.org/mailman/listinfo/gmx-users > > > Please search the archive at http://www.gromacs.org/search before > posting! > > > Please don't post (un)subscribe requests to the list. Use the > > > www interface or send it to [EMAIL PROTECTED] . > > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > > > > > _______________________________________________ > > gmx-users mailing list gmx-users@gromacs.org > > http://www.gromacs.org/mailman/listinfo/gmx-users > > Please search the archive at http://www.gromacs.org/search before > posting! > > Please don't post (un)subscribe requests to the list. Use the > > www interface or send it to [EMAIL PROTECTED] > > Can't post? Read > > http://www.gromacs.org/mailing_lists/users.php > > > > > -- > 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php >
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