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.
