Hi Bruno,
The only suggestion based on the GIST setup that I can give is maybe skip
the alignment step and try once more. There's an issue with Eww values in
aligned trajectories that sometimes produces odd values. That being said
your results are likely due to some corruption of the trajectory file
itself, the big red flag here is the inability to open the netcdf in vmd
and that when you convert to pdb the coordinates themselves are nan.
This simulation was setup using the equilibration and production parameters
outlined in the tutorial? Can you check previous steps (equilibration and
heating) to see if they too are unreadable/nan coordinates? I would also
check the log files associated with the simulations, it might be that in
one of the earlier steps the system blew up.
My guess based on this information is something has gone very wrong with
the production simulation and the nan energy results are GIST doing its
best to work with these strange coordinates, but more information will help
pin down the exact issue, if we can find the step/simulation that started
to produce these coordinates then it'd be easier to determine the specific
gremiln at play.
--Steve
On Tue, Dec 6, 2016 at 12:27 PM, Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
wrote:
> 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,
>
> 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 <
> brunofalcone.qo.fcen.uba.ar>
> > 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.
> >> http://ambermd.org/tutorials/advanced/tutorial25/
> >>
> >> 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 - 10:00:02 PST
