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

From: Bruno Falcone <>
Date: Tue, 6 Dec 2016 14:27:54 -0300

Hi Steve,

Thanks for getting back to me.

- these are calculations on another system

- solvent is TIP3P

- cpptraj version is 16.00

- 10000 frames

- the trajectory has been performed with the solute atoms restrained and
has been aligned prior to the gist calculation

- in this case I got nan in all voxels, but in other calculations I saw
nan in only some of them

- only the Eww has nan values

I checked the trajectories and I think I'm getting closer to finding out
what the problem may be. I used the NetCDF format for the trajectories
but I cannot visualize them with VMD. I converted them to pdb, and
cannot open them either. Inspecting the pdb file I can see that many of
the water coordinates have nan values in them. Perhaps the coordinate
numbers don't fit in the pdb columns so they appear as pdb? I converted
the frames to rst7 format and I also get nan in the coordinates.

Hope this helps,


On 06/12/16 13:59, Steven Ramsey wrote:
> 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)?
> Thanks,
> --Steve
> On Tue, Dec 6, 2016 at 9:40 AM, Bruno Falcone <>
> wrote:
>> 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 - 09:30:04 PST
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