Hi Sara, Assuming you have saved the script xtcrev.py:
# Get a clustered reference frame trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 200000 # Extract the first part of the trajectory trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 19999 # Reverse it ./xtcrev.py 1a.xtc > 1a-rev.xtc # Remove jumps trjconv -s cluster.gro -f 1a-rev.xtc -o 1a-rev-clus.xtc -pbc nojump # Reverse it again ./xtcrev.py 1a-rev-clus.xtc > 1a-clus.xtc # Extract the second part of the trajectory trjconv -s md.tpr -f md.trr -o 1b.xtc -b 200000 # Remove jumps trjconv -s cluster.gro -f md.trr -pbc nojump -o 1b-clus.xtc # Put the two together trjcat -f 1a-clus.xtc 1b-clus.xtc -o clustered.xtc # Hope it helps # Tsjerk On Fri, Dec 30, 2011 at 12:01 PM, mohammad agha <mra...@yahoo.com> wrote: > Dear gromacs users, > > At the first I thank from Tsjerk and Mark because of their answers to me but > unfortunately I don't understand that where is my mistake, still? > I work with MARTINI coarse-grained and I have a problem after -pbc nojump! > My simulation lasts 600 ns and 2 micelles are created from 200 ns and remain > during 400 ns, then my micelles isn't formed at the end of the trajectory. > My commands are: > 1- trjconv -f md.trr -s md.tpr -n index.ndx -e 600000 -pbc cluster -o 1.gro > In this step I viewed 2 micelles from 200 ns to 600 ns by ngmx -f 1.gro -s > md.tpr, so I have 2 micelles and -pbc cluster works me well and has been > removed box boundaries from my system but I saw very jumps in my system. > Okay? > 2- grompp -f md.mdp -c 1.gro -o 1.tpr -n index.ndx > 3- trjconv -f 1.gro -s 1.tpr -o 2.xtc -pbc nojump > After this step, had been removed jumps but I didn't see 2 micelles in 200 > ns, I saw that my monomers were collected as groups in the different places. > (This is bad and I don't know where is my mistake and what should I do to > solve my problem!) > After this, to solve my problem, I did: > 4- trjconv -f 2.xtc -s 1.tpr -o 3.xtc -pbc mol > In this step, I viewed 2 micelles from 200 ns to 600 ns and had been removed > jumps but existed boundaries of box, means my micelles that leaves a > simulation box by, say, the right-hand face, then enters the simulation box > by the left-hand face. > May I know can I start analysis of my system with 3.xtc? Is it good? If it > isn't good, Please help me for this problem with nojump. > > Thank you very much in advance > Best Regards > Sara > > -- > 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 -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands -- 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