Hi Sarah, You may file the bug report. You can submit a small part of the trajectory to reproduce the error :)
Cheers, Tsjerk On Wed, Dec 2, 2009 at 10:11 PM, Sarah Witzke <sawi...@student.sdu.dk> wrote: > Hi Tsjerk and others, > > This is a very good explanation! Thank you. Did you mean I should file a bug > report or are you doing it since you understand the code? > > Thank you all! > Sarah > > ________________________________ > > Fra: gmx-users-boun...@gromacs.org på vegne af Tsjerk Wassenaar > Sendt: on 02-12-2009 19:29 > Til: jalem...@vt.edu; Discussion list for GROMACS users > Emne: Re: SV: SV: SV: [gmx-users] g_saltbr > > > > Hi, > > Of course the real answer is in the code... > > if (bSep) { > snew(buf,256); > for(i=0; (i<ncg); i++) > for(j=i+1; (j<ncg); j++) { > if (nWithin[i][j]) { > sprintf(buf,"sb-%s:%s.xvg",cg[i].label,cg[j].label); > fp=xvgropen(buf,buf,"Time (ps)","Distance (nm)"); > ... > > So, a file is opened for each combination of charge(d) groups for > which the distance is lower than the cut-off, at least once in the > trajectory. The label is a property of the charge group, and is set > somewhere before: > > sprintf(buf,"%s%d",*(atoms->resname[resnr]),resnr+1); > cg[ncg].label=strdup(buf); > > Althogether, this just means that you have multiple charge(d) groups > per residue, which are assigned the same label. Let's see, a phosphate > and a choline, two residues, 2*2=4 possible salt bridges between them. > Seems to add up, doesn't it? Probably should be considered a bug > though. Better file it... > > Cheers, > > Tsjerk > > On Wed, Dec 2, 2009 at 7:10 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: >> >> >> Sarah Witzke wrote: >> >> <snip> >> >>> In each of the files are a set of distances as a function of time - it >>> does not seem that strange, that the size is equal then. >>> When I plot for instance the four .xvg files mentioned above I get four >>> different curves. Also "diff" lists that every line is different. >>> >>> I really don't understand what I'am doing wrong. >> >> I don't know that you are necessarily doing anything wrong, but it's hard to >> diagnose the potential problems without actually seeing what might be in >> those .xvg files. Can you post short snippets of a few of them, just to >> demonstrate what the difference is? I am wondering if there is so much >> memory required, that the calculation is dumping out the resulting data >> prematurely and therefore over-writing incomplete output files. Just a >> guess, but worth considering. >> >> -Justin >> >> -- >> ======================================== >> >> Justin A. Lemkul >> Ph.D. Candidate >> ICTAS Doctoral Scholar >> MILES-IGERT Trainee >> Department of Biochemistry >> Virginia Tech >> Blacksburg, VA >> jalemkul[at]vt.edu | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-us...@gromacs.org >> http://lists.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 gmx-users-requ...@gromacs.org. >> Can't post? Read http://www.gromacs.org/mailing_lists/users.php >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > Computational Chemist > Medicinal Chemist > Neuropharmacologist > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > > > -- > gmx-users mailing list gmx-us...@gromacs.org > http://lists.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 gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Computational Chemist Medicinal Chemist Neuropharmacologist -- gmx-users mailing list gmx-users@gromacs.org http://lists.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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php