Re: [AMBER] cpptraj gist: Eww energies

From: Daniel Roe <>
Date: Mon, 10 Aug 2015 11:12:57 -0600


On Mon, Aug 10, 2015 at 3:49 AM, Thomas Fox <> wrote:
> Eww values equal 0, but then 8 voxels with energies up to 300 kcal/mol. The
> neigboring voxels of these high-energy ones have what I would consider
> "normal" values.
> This behavior becomes extremely pronounced when I use a larger grid for my
> gist calculation (for a 41x41x41 grid with a spacing of 0.5A, I get energy
> values up to 1E19, and about 13000 of the 68921 data points have a Eww-norm
> > 100 kcal/mol.
> parm
> trajin cb7_solv.crd
> trajin 1 5000
> autoimage origin
> rmsd CUC :1 first

I would bet the large values you are seeing are the result of
collisions caused by RMS-fitting after imaging (as mentioned by
Crystal). The problem is that GIST uses imaged distances in it's
calculations, but once you RMS-fit a system it is almost always
rotated away from the original unit cell axes and so imaging no longer
works properly (which is why cpptraj prints out a warning to this
effect when RMS-fitting a system with PBC). For small rotations the
effect may not be noticeable, but it's there. The effect is more
pronounced for atoms farther away from the rotation which is why
increasing the grid size gives you more clashes.

As implied by Crystal probably the best way to ensure you get a well
behaved grid at the moment is to put some mild positional restraints
on your solute. On my current to-do list is to have a grid which can
"move" with the solute using the RMS results - I hope to have this
implemented soon.

Hope this helps,


> gist gridcntr 0. 0. 0. griddim 21 21 21 gridspacn 0.5 out gist_21_05.out
> run
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Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Mon Aug 10 2015 - 10:30:02 PDT
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