[gmx-users] g_msd and pbc

[Tsjerk Wassenaar]

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