From: Jonathan Gough <>
Date: Tue, 10 Nov 2015 10:28:46 -0500

Hi Yulian Gavrilov,

What Steve said is spot on. In the present implementation of gist-cpptraj,
the energy calculations utilize the periodic box dimensions (I believe it's
from the first frame) when calculating energy. When one uses the cpptraj
rms function the entire box is rotated at every frame. Therefore the change
in box position is lost. As a result the energy calculations are all wrong.

How were you planning on calculating the desired values(dA, dTS, dE)?

If you can simply calculate the values by integrating over the entire box
volume, you could run the simulation restrained and unrestrained. Then,
make your gist box large enough (probably best to do the same/identical
size about both simulations) to encompass the peptide and run gist. Then
you could utilize the post processing tool, gistpp, to get the values you
wish for each system and then compare.

you can find the instructions for gistpp on the last page of the tutorial:

You can grab the code from the above page or from github.

Don't hesitate to reach out if you need additional help.


On Tue, Nov 10, 2015 at 10:04 AM, Steven Ramsey <> wrote:

> 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 <>
> wrote:
> > 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
AMBER mailing list
Received on Tue Nov 10 2015 - 07:30:05 PST
Custom Search