Thanks a lot for the reply. But I am getting different results with the two .tpr files (first and last) using the following commands:
trjconv -s *first.tpr *-f test.xtc -o str.gro -dump 10000 -pbc nojump trjconv -s *last.tpr* -f test.xtc -o str.gro -dump 10000 -pbc nojump So which .tpr file should I use? Thanks, Anirban On Sat, Dec 4, 2010 at 12:29 PM, Mark Abraham <mark.abra...@anu.edu.au>wrote: > On 4/12/2010 4:33 PM, Anirban Ghosh wrote: > >> 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? >> > > Since you're not using the coordinates in the .tpr file to extract the last > frame and map its coordinates onto the .tpr's atom names, it can't matter > what they are. > > Mark > > > 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 >
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