Hi Peter,
You certainly can run GIST on a clustered trajectory and you should find
similar/ good convergence rates, it would depend on the number of frames in
your cluster, but my hunch on typical clustering protocols is that at least
your top cluster will perform well.
The caveat is that sometimes structures that have been aligned lose system
information used in GIST energy calculations, producing strange
(arbitrarily high energy) results. Here's an archived response on the
matter: http://archive.ambermd.org/201508/0155.html .
We're aware of this issue and working to fix it, the good news is that all
other terms calculated in GIST should behave normally on a clustered
system.
--Steve
On Tue, Mar 1, 2016 at 2:23 AM, <peter.schmidtke.discngine.servier.com>
wrote:
> Hello,
>
> I wondered if there is any literature or advice whether gist calculations
> could potentially be done on clustered conformations rather than fixed
> proteins and lengthy trajectories. Basically I have very long trajectories
> that I cluster around an area of interest and I end up with quite a large
> number of frames in a "stable" state.
> I guess the best way would be to check for convergence with this method
> versus a constrained trajectory, but I wanted to know if somebody actually
> did that already or not.
>
> Thanks in advance for your reply.
>
> Peter Schmidtke
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>
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Received on Tue Mar 01 2016 - 07:00:03 PST
