[gmx-users] g_msd for many molecules

[Justin Lemkul]

On 5/1/13 8:40 AM, George Patargias wrote:
> Hello
>
> I am trying to calculate the MSD of 8 molecules in a lipid bilayer with
> g_msd. If I include the atoms of all these 8 molecules as a single group
> in the index file, will g_msd calculate the MSD of the center of mass of
> them or it will average over all atoms?
>

The calculation considers all the atoms, not just their COM.

-Justin

-- 
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Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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