Re: [AMBER] Regarding GIST calculation

From: Steven Ramsey <>
Date: Fri, 1 Jul 2016 10:12:03 -0400

Hello Atul,

The total orientational entropy for your system is pretty high, I would
figure this is likely due to your selecting 1000 frames. The orientational
entropy calculations in GIST are not well converged until about 30000
frames of sampling. This under-sampling can reasonably lead to
unrealistically high entropy values thus giving a system sum that seems
incredibly high (1837).

The energy is a different problem, the energy calculations in GIST converge
pretty quickly, however there is a known bug where if the user submits a
system that has been aligned the energy function spits out high energies.
Here is a previous post regarding this issue that may have more detail:

If your system is not aligned or un-restrained, then there is something
else afoot and I would want more information to determine where the issue
is, but thus far we have seen high energies when dealing with unrestrained
systems (bug).

Hope this helps,


On Fri, Jul 1, 2016 at 1:51 AM, ATUL KUMAR <> wrote:

> Dear Amber user, I am running GIST calculation for my system to calculation
> solvation properties of my bio-molecule of interest. But the values whichj
> I am getting for oriantation entropy and water-water interaction potential
> looks very unreal:
> here are the out put of my ptraj stript
> Maximum number of waters found in one voxel for 1000 frames = 18
> Total referenced orientational entropy of the grid: dTSorient = 1837.63288
> kcal/mol, Nf=1000
> Total referenced translational entropy of the grid: dTStrans = -656.56374
> kcal/mol, Nf=1000
> Total water-solute energy of the grid: Esw = -6883.98185 kcal/mol
> Total unreferenced water-water energy of the grid: Eww =
> 36968874607662650621952.00000 kcal/mol
> *Atul Kuamr jaiswal*
> Research Scholar
> School of Computational and Integrative Sciences
> Centre for Computational Biology and Bioinformatics (CCBB)
> JNU,New Delhi
> India.
> _______________________________________________
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Received on Fri Jul 01 2016 - 07:30:02 PDT
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