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:
http://archive.ambermd.org/201508/0155.html
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,
--Steve
On Fri, Jul 1, 2016 at 1:51 AM, ATUL KUMAR <atul44_sit.jnu.ac.in> 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
>
> ACTION OUTPUT:
> 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
