[gmx-users] (no subject)

[Erik Marklund]

Hi,

Average structures are typically unphysical and rarely meaningful. Consider for instance the average structure of a spinning methyl group. Representative structures can be produced by clustering the frames in a trajectory and selecting the cluster centroids. See g_cluster.

Kind regards,
Erik

Erik Marklund, PhD
Postdoctoral Research Associate

Department of Chemistry
Physical & Theoretical Chemistry Laboratory
University of Oxford
South Parks Road
Oxford
OX1 3QZ

On 24 Sep 2014, at 08:38, Mahboobeh Eslami <mahboobeh.eslami at yahoo.com> wrote:

> Hi GMX users
> what command should I use to obtain the average structure in pdb format for two nanosecond of the end of simulation.Thank you sincerely for your help
> -- 
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