[gmx-users] MSD

Justin A. Lemkul jalemkul at vt.edu
Wed Dec 23 19:58:01 CET 2009

Quoting afsaneh maleki <maleki.afsaneh at gmail.com>:

> Hi,
> I am working on the simulation of protein memberane.
> How can I calculate MSD (mean squar displacement) of bond lipid ( as those
> phosphate atomes are written 0.35 nm of protein)?
> I know that I must use g_msd for calculating, but I need “index file” that
> is included phosphate atoms within 0.35 nm of protein. how can I obtain this
> index file

Please see g_dist -dist.


> thanks in advance,
> Afsaneh Maleki


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080


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