You seem to be following http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions, which is good. But it's hard to help when we don't know what you think "doesn't work" means. Make sure that the things you think are whole in md_0_1.tpr actually are. Visualize your intermediate stages of 1) to see where the issue arises. If you need to, upload some pictures to a file sharing service that show what the input and unsatisfactory output was.
Mark On Mon, May 19, 2014 at 3:15 PM, Vito Genna <vito.ge...@iit.it> wrote: > Hi to everybody, > > My name is Vito and I would like to share with you (and discuss also) the > problems that I have found during my TRJs analysis. > I have a system made by: Protein + dsDNA + Ligand. I obtained my single > precision trajectory in a .xtc file. > Well, I'd like to analyze my TRJs using VMD due to its intrinsic velocity > in calcuating (Distances, angles, RMSD and so on) but I cannot do it > because I encounter a serious issue with the visualization (pbc problems as > you surely know) > To try to avoid the problem I've used several protocols, without success: > > 1) > > a) trjconv_mpi -f md_0_1.part0001.xtc -o md_0_1-whole.xtc -s md_0_1.tpr > -pbc whole (on the entire system) > b) trjconv_mpi -f md_0_1-whole.xtc -o md_0_1-nojump.xtc -s md_0_1.tpr -pbc > nojump > (on the entire system) > c) trjconv_mpi -f md_0_1-nojump.xtc -o md_0_1-fit.xtc -s md_0_1.tpr -fit > progressive (on Protein only) > > It does not work. > > 2) > > a) trjconv_mpi -f (as the previous one) -pbc mol -ur compact -center -o > compact.xtc > > It does not work as well. > > 3) Option 2 changing the flag -pbc mol with -pbc res > > It does not work. > > New idea? New possible combo? > > Thanks in advance for your replies. > > All the best > > Vito > > > > > Vito Genna, PhD-Fellow > Italian Institute of Technology > Drug Discovery and Development department > Via Morego 30, 16163 Genoa, Italy > > > ------------------------------------------------------------------------------------------------------------- > The process of scientific discovery is, in effect, a continual flight from > wonder. > Albert Einstein > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.