[gmx-users] Re: Representative structure

[Ing. Vojtech Spiwok]

> 
> 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