[gmx-users] Diffusion beyond periodic boundary

[Tsjerk Wassenaar]

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
> >> >
> >> >
> >> > --
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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
> >> --
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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
> ====================
>
>
> --
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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