Dear Tsjerk Thank you for reply. I will make PDB using "-pbc nojump" and rewind only the selected molecules by own program.
Thank you Kenji ----- Original Message ----- >> From: Tsjerk Wassenaar <tsje...@gmail.com> >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> Date: 2013-02-09 19:17:12 >> Subject: Re: [gmx-users] Diffusion beyond periodic boundary >> >> Hi Kenji, >> >> That's not possible. But why would you need that? It's not very hard to >> make the changes required in gmx_trjconv.c >> >> Cheers, >> >> Tsjerk >> >> On Sat, Feb 9, 2013 at 9:37 AM, Kenji Mochizuki <kmo...@ims.ac.jp> wrote: >> >> > Dear Tsjerk >> > >> > Thank you very much, >> > "-pbc nojump" works well. >> > >> > Is it possible to select the specific molecule for "-pbc nojump" ? >> > For example, >> > the coordinates of water molecules are rewind and the LJ particles are NOT >> > rewind ? >> > >> > Regards >> > >> > Kenji >> > >> > ----- Original Message ----- >> > >> From: Tsjerk Wassenaar <tsje...@gmail.com> >> > >> To: Discussion list for GROMACS users <gmx-users@gromacs.org> >> > >> Date: 2013-02-09 17:24:23 >> > >> Subject: Re: [gmx-users] Diffusion beyond periodic boundary >> > >> >> > >> Hi Kenji, >> > >> >> > >> You can remove the jumps/rewinds using 'trjconv -pbc nojump'. >> > >> >> > >> Cheers, >> > >> >> > >> Tsjerk >> > >> >> > >> On Sat, Feb 9, 2013 at 4:45 AM, Kenji Mochizuki <kmo...@ims.ac.jp> >> > wrote: >> > >> >> > >> > Dear All >> > >> > >> > >> > I have performed MD run with periodic boundary condition, >> > >> > which system is consist of water and LJ particles. >> > >> > >> > >> > I would like to know the time dependence of the dislocated distance >> > >> > (diffusion) from the starting time (t=0). >> > >> > Firstly, I made pdb file of the trajectory, then calculated the >> > distance >> > >> > from pdb file. >> > >> > >> > >> > However, when the particle goes beyond periodic boundary, >> > >> > the x-y-z coordination is rewind into the box size. >> > >> > So, the dislocated distance is wrong. >> > >> > >> > >> > Could you please tell me how to calculate the dislocated distance >> > >> > accurately ? >> > >> > >> > >> > Best regards >> > >> > >> > >> > Kenji >> > >> > >> > >> > >> > >> > -- >> > >> > 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 >> > >> Biocomputing Group >> > >> Department of Biological Sciences >> > >> 2500 University Drive NW >> > >> Calgary, AB T2N 1N4 >> > >> Canada >> > >> -- >> > >> 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 >> > >> >> > >> >> > >> >> > >> > ==================== >> > National Institutes of Natural Sciences >> > Institute for Molecular Science >> > >> > Kenji Mochizuki >> > >> > e-mail: kmo...@ims.ac.jp >> > phone: 0564-55-7394 >> > ==================== >> > >> > >> > -- >> > 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 >> Biocomputing Group >> Department of Biological Sciences >> 2500 University Drive NW >> Calgary, AB T2N 1N4 >> Canada >> -- >> 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 >> >> >> ==================== National Institutes of Natural Sciences Institute for Molecular Science Kenji Mochizuki e-mail: kmo...@ims.ac.jp phone: 0564-55-7394 ==================== -- 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
