[gmx-users] average structure

larifsofiene larifsofiene at gmail.com
Mon Oct 31 09:39:45 CET 2011

i'm doing a MD simulation for a monomeric protein over 10 ns, my 
question is :

* for my MD how do i know that it has equilibrated and suitable for 
study ?,is it RMSD , Radius of gyration and potential energy stability 
enough ? OR should i look for other parameters and do multiple 
simulation with the same results ?

* for simulation structure study should i use an average structure 
(g_covar or grmsf) OR should i use the last trajectory from the 
simulation (the 10 th ns trajectory )

*if i use average structure should i delete hydrogen before looking for 
hydrogen bonds ?,because average structure with it's original H give 
abnormal H bonds.

Thanks very much :)

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