[gmx-users] Diffusion beyond periodic boundary

[Kenji Mochizuki]

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 <tsjerkw at gmail.com>
>> To: Discussion list for GROMACS users <gmx-users at 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 <kmochi at 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 <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
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>> > >>
>> > >>
>> > >>
>> > >> --
>> > >> 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
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>> > >>
>> > >>
>> >
>> > ====================
>> > National Institutes of Natural Sciences
>> >   Institute for Molecular Science
>> >
>> >   Kenji Mochizuki
>> >
>> >   e-mail: kmochi at ims.ac.jp
>> >   phone: 0564-55-7394
>> > ====================
>> >
>> >
>> > --
>> > gmx-users mailing list    gmx-users at gromacs.org
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>> 
>> 
>> 
>> -- 
>> 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
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>> 
>> 

====================
National Institutes of Natural Sciences
  Institute for Molecular Science

  Kenji Mochizuki

  e-mail: kmochi at ims.ac.jp
  phone: 0564-55-7394
====================