Thanks a lot Justin for the reply. Yes, I understand that. But ideally which structure should be used as the reference, in a general, the starting structure or the end structure? like when I an using trjconv to dump my last frame (with "-pbc nojump"), which .tpr file should I use to get the exact picture of what has happened to my protein at the end of the simulation. Should I use the first .tpr file or the last .tpr file?
Thanks a lot again. Anirban On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: > >> Hi ALL, >> >> Its a very basic question but still... >> When we calculate RMSD (or any other parameter) using the g_rms command, >> we need to supply the .tpr file with -s option. Now suppose if I have a >> total 20 ns simulation with 4 breaks (i.e 5 ns in each run), then there will >> be 4 .tpr files. So at the end of 20 ns if I wish to calculate RMSD, then >> which .tpr file should I suppy to g_rms, the first one or the last one? We I >> run g_rms with the two .tpr files, I get different results. So which one >> should be used? Any suggestion is welcome. >> >> > Use the one that contains the structure you wish to serve as your > reference. > > -Justin > > >> Thanks, >> >> Anirban >> >> > -- > ======================================== > > 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-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/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/Support/Mailing_Lists >
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