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

From: Bruno Falcone <>
Date: Tue, 6 Dec 2016 15:44:06 -0300

Hi Steve and Dan,

Thank you very much for your suggestions. The problem arose indeed due
to problems in the trajectories, which originated from establishing the
restraintmask as !:WAT instead of !(:WAT). With the former the
restraints were not working.

I'm re-running the calculations now, will let you know how it goes.


On 06/12/16 15:38, Daniel Roe wrote:
> On Tue, Dec 6, 2016 at 12:27 PM, Bruno Falcone
> <> wrote:
>> 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
> Having 'nan' in your coordinates is never a good thing. Do you get any
> warnings during trajectory process of the format "Warning: Set X
> coords 1 & 2 overlap at origin; may be corrupt."? You may want to run
> the 'check' command to look for bad coordinates throughout your system
> (although be aware this can be an expensive and slow calculation, even
> when using cpptraj.OMP). If you do have bad frames you can use 'check'
> in conjunction with 'skipbadframes' to skip these problem frames.
> Hope this helps,
> -Dan
>> 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,
>> Thanks,
>> Bruno
>> 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
>>>> _______________________________________________
>>>> AMBER mailing list
>>> _______________________________________________
>>> AMBER mailing list
>> _______________________________________________
>> AMBER mailing list

AMBER mailing list
Received on Tue Dec 06 2016 - 11:00:03 PST
Custom Search