[gmx-users] Re: Representative structure

Ing. Vojtech Spiwok Vojtech.Spiwok at vscht.cz
Mon Oct 4 11:49:41 CEST 2004

> Hi all,
> How can I get a "representative structure" of the end of a MD 
> trajectory? Should I average the structures of the last time frames?
> Thanks in advance,
> Bests,
> Ruben
An averaged structure has incorrect stereochemistry. For example if
methyl group rotates during the dynamics in averaged structure it would
look like a upside down umbrella. On the other hand for example ligand
docking to such structure might be succesful. Who knows.

Vojtech Spiwok

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