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 <[email protected]> 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 <[email protected]> > >> To: Discussion list for GROMACS users <[email protected]> > >> 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 <[email protected]> > 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 [email protected] > >> > 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 [email protected]. > >> > * 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 [email protected] > >> 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 [email protected]. > >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > >> > >> > >> > > ==================== > National Institutes of Natural Sciences > Institute for Molecular Science > > Kenji Mochizuki > > e-mail: [email protected] > phone: 0564-55-7394 > ==================== > > > -- > gmx-users mailing list [email protected] > 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 [email protected]. > * 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 [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
