Thanks a lot for the reply. Actually I am running a protein in lipid bilayer. Now I want to calculate the thickness of the bilayer at the end of the simulation. So for that I want the last structure (.gro) file. So I am trying to dump the last structure using trjconv (with -pbc option). So to do this which .tpr file should I supply to trjconv, the first one or the last one?
Thanks again. Anirban On 12/4/10, Justin A. Lemkul <jalem...@vt.edu> wrote: > > > Anirban Ghosh wrote: >> 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? > > That's up to you to decide based on what you need to measure. Do you want > the > RMSD relative to your starting (i.e. crystal/NMR) structure, or are you > trying > to study how a protein folds, in which case you'd use the native (end) > state? > >> 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? >> > > I don't understand what you mean. "What has happened" is an entire > trajectory, > not a snapshot. > > -Justin > >> Thanks a lot again. >> >> Anirban >> >> On Fri, Dec 3, 2010 at 7:35 PM, Justin A. Lemkul <jalem...@vt.edu >> <mailto: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 <http://vt.edu> | (540) 231-9080 >> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin >> >> ======================================== >> -- >> gmx-users mailing list gmx-users@gromacs.org >> <mailto: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 >> <mailto:gmx-users-requ...@gromacs.org>. >> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > > -- > ======================================== > > 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 > -- 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
