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