[gmx-users] g_msd for many molecules

[Dr. Vitaly Chaban]

The resulting MSD will correspond to the average from individual atoms.

Calculating MSD of an individual atom and ascribing it to a [small]
molecule, which this atom belongs to, is reasonable. Assuming that averaged
MSD from atoms correspond to the cluster they form is not.


Dr. Vitaly Chaban




On Wed, May 1, 2013 at 2:40 PM, George Patargias <gpat at bioacademy.gr> 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?
>
>
> Thanks
> George
>
>
> Dr. George Patargias
> Postdoctoral Researcher
> Biomedical Research Foundation
> Academy of Athens
> 4, Soranou Ephessiou
> 115 27
> Athens
> Greece
>
> Office: +302106597568
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