[gmx-users] (no subject)

Erik Marklund erik.marklund at chem.ox.ac.uk
Wed Sep 24 10:27:29 CEST 2014


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 Marklund, PhD
Postdoctoral Research Associate

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

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
> -- 
> Gromacs Users mailing list
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list