Re: [AMBER] GIST: nan (not a number) in unreferenced water-water energy of the grid

From: Steven Ramsey <>
Date: Tue, 6 Dec 2016 11:59:50 -0500

Hi Bruno,

That's a strange output for GIST. Some information would help me get to the
bottom of this issue and therefore make suggestions on how to resolve it
(the first question will likely clarify the remaining questions if the
answer is yes):

Are these GIST calculations performed within the tutorial itself? (meaning
the calculations are run on the given files/trajectories and are exactly
following the instructions)
What solvent model is in use?
Which version of GIST is in use?
How many frames are being analyzed by GIST?
Was there any alignments being used before using GIST?
Are we seeing nan's in every voxel or a few here and there? (both are bad,
but it will help me figure out what went wrong)
Are there any other files with nan values (particularly Esw)?



On Tue, Dec 6, 2016 at 9:40 AM, Bruno Falcone <>

> Hi, I'm performing Grid Inhomogeneous Solvation Theory (GIST)
> calculations with cpptraj, of small organic compounds in water.
> I followed the instructions in the GIST tutorial and performed a
> restrained MD to then analyse with GIST.
> Although most of the calculations succeed, I'm getting "nan" (not a
> number) in the "Total unreferenced water-water energy of the grid: Eww"
> term. Checking the .dx files, this arises from the gist-Eww-dens.dx file
> containing all nan in the output.
> Was wondering why this might be the case, and if you could point out to
> any suggestions to fix this problem.
> Thanks for your help,
> Bruno
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Received on Tue Dec 06 2016 - 09:30:02 PST
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