Hi Steven, Don't use -ur compact in the first step and see if that solves the problem.
Oh, and be sure that the thing is not just diffusing. There was a thread lately where a diffusing ligand drove someone mad trying to remove the 'jumps'. Cheers, Tsjerk On Mon, Nov 7, 2011 at 3:08 PM, Steven Neumann <s.neuman...@gmail.com> wrote: > Dear Gmx Users, > > I know that this problem has been discussed may times but I cannot find the > solution to get rid of pbc in my system: protein and ligand. I followed the > workflow: > > > 1. First make your molecules whole if you want them whole > > trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc > > 2. Cluster your molecules/particles if you want them clustered > > 3. Extract the first frame from the trajectory as reference for > removing jumps if you want to remove jumps. > > trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb > > 4. Remove jumps if you want to have them removed using the first frame > > trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc > > 5. Center your system using some criterion. Doing so shifts the system, > so don't use trjconv -pbc nojump after this step. > > trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc > > 6. Put everything in some box. > > trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc > > 7. Fit if desired and don't use any PBC related option afterwards. > > trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o > mdfinal.xtc > > > > I used SYSTEM everywhere as output orinput. However, my ligand is still > jumping like a fly around the stable protein. Do you have any suggestions? > > > > Steven > > -- > 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
