From: Steven Ramsey <>
Date: Tue, 10 Nov 2015 10:04:56 -0500

You can certainly analyze solvent properties around a flexible system,
however there are some things to keep in mind:

The GIST grid itself will not move with your system (neither will each
individual voxel), therefore the sampling in certain voxels, particularly
those that are near your solute, will have lower sampling due to solute
fluctuations, which may effect several quantities (g(O), S, E).

You could align the flexible system (or cluster it as you suggested), but
then this may introduce another potential issue which was brought up in
this thread:

Entropy should be fine on a clustered system, provided there's enough
frames to sample from. The lesser populated clusters may produce
thermodynamics that are not-trustworthy (meaning not converged, but that
applies to all quantities not just S).

So to summarize a bit, it is definitely possible to analyze a flexible
system, but it is more troublesome than a rigid one. A lot depends on just
how flexible it is. Either choice (running GIST on a flexible simulation or
a clustered one) will map solvation data to the defined voxels, so you can
potentially play around with it and see what works for your system.

Hope this helps,

--Steven Ramsey

On Tue, Nov 10, 2015 at 3:24 AM, Yulian Gavrilov <>

> Dear all,
> I have a question about GIST.
> In the tutorial and manual it is written that the protein should be rigid
> in order to use GIST to analyze water around it.
> Is there any way to analyze hydration water around a flexible molecule?
> I would like to compare the thermodynamic parameters (dA, dTS, dE) of
> hydration water around the flexible and rigid version of a peptide. Is
> there any way to do it?
> I use AmberTools15.
> Only idea that I have is to devide the output trajectory of the flexible
> peptide into several clusters based on RMSD, so that within the cluster the
> flexibility of a peptide will be minimal. Then I can use GIST for each
> cluster separately. But this way I won't get the right entropy values,
> right?
> Thank you in advance for any ideas!
> --
> Sincerely,
> Yulian Gavrilov
> _______________________________________________
> AMBER mailing list
AMBER mailing list
Received on Tue Nov 10 2015 - 07:30:03 PST
Custom Search