[gmx-users] Diffusion beyond periodic boundary

[Kenji Mochizuki]

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 <tsjerkw at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at 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 <kmochi at 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 at 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-request at 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 at 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-request at 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: kmochi at ims.ac.jp
  phone: 0564-55-7394
====================