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

From: Daniel Roe <>
Date: Wed, 7 Dec 2016 16:07:50 -0500

On Wed, Dec 7, 2016 at 2:41 PM, Bruno Falcone
<> wrote:
> It seems that the water coordinates are getting very large so they don't
> fit into the rst7 or other ascii based formats, but they do in the
> netcdf format. I guess GIST internally uses the ascii trajectory format
> coordinate size limit?

No, all coordinate calculations in GIST (and in cpptraj as a whole)
are done with full double precision. As long as there are no issues
with your input coordinates there should be no coordinate-based issues
with the GIST calculation.

> I tried centering the netcdf file with these cpptraj commands but the
> 'nan' remain in the coordinates (when I convert them to rst7 to test that).

Did you try testing the frames converted thusly with the 'check'
command? This can tell you if the problem is with the trajectory

> I also tried to align the centered trajectory with rms but the problem
> persists.

RMS-fitting is not recommended prior to GIST (or with anything that
may use imaged distances). Rotating coordinates will mess up image

> Any idea how I can solve this issue and obtain a trajectory that can be
> converted to ascii based so that I can re-run gist?

I recommend checking some of your problem frames with the cpptraj
'check' command to make sure they are not the issue.


> Thanks,
> Bruno
> On 06/12/16 15:44, Bruno Falcone wrote:
>> 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.
>> Bruno
>> 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
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Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Wed Dec 07 2016 - 13:30:02 PST
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