Thanks <meta charset="utf-8">Tsjerk for the information. It would be very nice if you can elaborate it. I am unable to understand. <br clear="all"><br>--<br>Chandan kumar Choudhury<br>NCL, Pune<br>INDIA<br>
<br><br><div class="gmail_quote">On Thu, Dec 8, 2011 at 12:10 AM, Tsjerk Wassenaar <span dir="ltr"><<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
Hi Chandan,<br>
<br>
Pretty simple; you just take the smallest distance between the time<br>
points in the periodic system.<br>
<br>
Cheers,<br>
<br>
Tsjerk<br>
<div><div class="h5"><br>
On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury <<a href="mailto:iitdckc@gmail.com">iitdckc@gmail.com</a>> wrote:<br>
><br>
> Dear gmx_users,<br>
><br>
> I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the<br>
> PBC. e.g. If I want to calculate the lateral diffusion of a lipid bilayer<br>
> and at some point of the trajectory, some lipid molecules, due to PBC in the<br>
> lateral direction, might pop out from one side of the box and re-ener from<br>
> the other side. I such a situation it should show a very lage msd, but<br>
> actually in the g_msd code, this fact is taken care of. Can some one<br>
> explain, how is this effect taken care of.<br>
><br>
><br>
> Chandan<br>
> --<br>
> Chandan kumar Choudhury<br>
> NCL, Pune<br>
> INDIA<br>
><br>
</div></div>> --<br>
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<span class="HOEnZb"><font color="#888888"><br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
<br>
post-doctoral researcher<br>
Molecular Dynamics Group<br>
* Groningen Institute for Biomolecular Research and Biotechnology<br>
* Zernike Institute for Advanced Materials<br>
University of Groningen<br>
The Netherlands<br>
--<br>
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