On 1 Mar, 2012, at 1:01, Steven Neumann <s.neuman...@gmail.com> wrote:
> 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? You may wanna try Trjconv -f md298SKIP4.xtc -s md298.tpr -pbc whole -ur compact -o pdbs.pdb -dt 1000 Please change dt if necessary. > > 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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