Re: [AMBER] GIST: convergence of the translational entropy term

From: Steven Ramsey <>
Date: Fri, 11 Nov 2016 11:43:15 -0500

Hi Sergey,

I think the initial drop in entropy you're seeing in your analysis is
indeed an artifact due to low sampling. At very low frame counts (under
1000 or so) the nearest neighbor algorithm used to solve entropies will
provide strange results due to there being a very low number of waters (and
therefore neighbor distances) to consider.

We recently evaluated GIST convergence rates in the cpptraj software
release study (doi: 10.1002/jcc.24417) and found that entropies converge
within 30000 frames (sampled every ps). This may be system specific, but is
a reasonably good guess for most studies.

Hope this helps, best of luck!


On Fri, Nov 11, 2016 at 9:28 AM, Sergey Samsonov <> wrote:

> Dear AMBERs,
> I'm calibrating some GIST calculations. In particular, I'm checking how a
> number of frames (equidistantly distributed through the equilibrated
> simulation) taken for GIST calculations affects the values of GIST energy
> components. The reason to do this is to find an optimal length of my
> simulations (and a number of frames to analyze with GIST) for a system I
> study so that the values I obtain are converged. I found a common feature
> independently of regions, sizes a box used for GIST and lengths of the
> simulations within the ranges I'm working in. So E(sw), E(ww) and
> TS(orientational) converge very similarly: the values go down monotonically
> with the increase of number of frames taken into account for the
> calculations and converge for several thousand of frames (exact number
> depends on the system and simulation type). This result is something one
> can expect. However, TS(translational) behaves essentially differently: its
> value drops when increasing the number of analyzed frames to ~200 and then
> it goes up again (one of the examples is attached for 10000 frames from 100
> ns long simulation). What could be the reason for such a non-monotonic
> behaviour? Is the decrease observed simply due to an artifact of the
> calculations when the number of frames too low?
> Thank you very much and cheers,
> Sergey
> --
> Sergey A. Samsonov
> Postdoctoral researcher
> Structural Bioinformatics
> Biotechnology Center
> Tatzberg 47-51
> 01307 Dresden, Germany
> Tel: (+49) 351 463 400 83
> Fax: (+49) 351 463 402 87
> E-mail:
> Webpage:
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Received on Fri Nov 11 2016 - 09:00:03 PST
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