you can do clustering for both simulations and compare population for each
cluster. Search Amber 15 manual for cpptraj clustering.
Look at Figure 4 in this for example:
http://pubs.acs.org/doi/full/10.1021/ct600263e
Hai
On Fri, Jul 10, 2015 at 3:35 PM, Xing <stecue.gmail.com> wrote:
> Dear All,
>
> I have obtained two equilibrium trajectories of a protein using two
> slightly different approaches. Is there a rigorous way to show that the
> structures of the two trajectories are statistically the
> same (and therefore the two results of the approaches are identical)? RMSD
> with respect to their overall averaged structure and individual averages? I
> think the energy cannot be compare because the
> number of water molecules are different when solvating in xleap.
>
> --
> Best wishes,
>
> Xing
>
>
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Received on Fri Jul 10 2015 - 13:00:04 PDT
