[gmx-users] g_msd and pbc

[Chandan Choudhury]

Thanks Tsjerk for the information. It would be very nice if you can
elaborate it. I am unable to understand.

--
Chandan kumar Choudhury
NCL, Pune
INDIA


On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Chandan,
>
> Pretty simple; you just take the smallest distance between the time
> points in the periodic system.
>
> Cheers,
>
> Tsjerk
>
> On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury <iitdckc at gmail.com>
> wrote:
> >
> > Dear gmx_users,
> >
> > I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
> > PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer
> > and at some point of the trajectory, some lipid molecules, due to PBC in
> the
> > lateral direction, might pop out from one side of the box and re-ener
> from
> > the other side. I such a situation it should show a very lage msd, but
> > actually in the g_msd code, this fact is taken care of. Can some one
> > explain, how is this effect taken care of.
> >
> >
> > Chandan
> > --
> > Chandan kumar Choudhury
> > NCL, Pune
> > INDIA
> >
> > --
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>
>
> --
> Tsjerk A. Wassenaar, Ph.D.
>
> post-doctoral researcher
> Molecular Dynamics Group
> * Groningen Institute for Biomolecular Research and Biotechnology
> * Zernike Institute for Advanced Materials
> University of Groningen
> The Netherlands
> --
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