Thank you all! That helped a lot! Steven
On Wed, Feb 29, 2012 at 5:17 PM, Vedat Durmaz <dur...@zib.de> wrote: > ** > i always did it (successfully) with one single command: > > trjconv -f md.trr -s md.tpr -o mdCompact.trr -pbc mol -ur compact -n > ../../index.ndx > > > regards > vedat > > > Am 29.02.2012 18:01, schrieb Steven Neumann: > > Dear Gmx Users, > > I am run a simulation with Gromacs 4.5.4. of my protein and 15 ligands. > The problem I face is PBC which I cannot get rid of. I used: > > > 1. First make your molecules whole if you want them whole (system). > > trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -o md298whole.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 md298.trr -s md298.tpr -dump 0 -o 1stframe.pdb > > 4. Remove jumps if you want to have them removed using the first > frame (system) > > trjconv -f md298whole.xtc -s 1stframe.pdb -pbc nojump -o md298nojump.xtc > > > > So the trajecory of my ligands is smooth but they do do bind to the > different periodic images. As i know it is impossible to obtain the proper > trajectory of all of them I just want to obtain the realistic final > positions of my system to extract pdb file for further umbrella sampling. > 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 >
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