Re: [AMBER] cpptraj gist: Eww energies

From: Tom Kurtzman <>
Date: Mon, 10 Aug 2015 17:59:44 +0300

Hi Tom,

Someone else had this same problem when running simulations on an
unrestrained solute.

It turned out that the familar option was off when imaging the box. Will
you try that?

image origin center familiar


Tom Kurtzman, Ph.D.
Assistant Professor
Department of Chemistry
Lehman College, CUNY
250 Bedford Park Blvd. West
Bronx, New York 10468

---------- Forwarded message ----------
From: Thomas Fox <>
Date: Mon, Aug 10, 2015 at 12:49 PM
Subject: [AMBER] cpptraj gist: Eww energies


   I started playing around with the gist functionality in cpptraj and
   it would be a good idea to try to reproduce the original cucurbituril
   results of Nguyen, Young and Gilson from JCP 137, 044101 (2012).

   In general, this works nicely, after 500ns of standard simulation, with
   total 5000 snapshots, I get plots that look very similar to what Nguyen
   al report in their paper.

   However, when looking at the Eww-norm.dx data, I see a number of voxels
   have a extremely high energy. As a first attempt, I have used a 21x21x21
   grid with a spacing of 0.5 (this doesnt even encompass all of the
   cucurbituril) - a histogrm of the Eww data shows a somewhat skewed, but
   still approximate Gaussian distribution for values below 0, a large peak
   Eww values equal 0, but then 8 voxels with energies up to 300 kcal/mol.
   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
   gist calculation (for a 41x41x41 grid with a spacing of 0.5A, I get
   values up to 1E19, and about 13000 of the 68921 data points have a
> 100 kcal/mol.

   My simulation box is about 35x35x35A, i.e. for larger gist grids one
   close(r) to the edge of the box, so there might be some edge/PBC effects
   (really??), especially as these high energy voxels tend to concentrate at
   the edges of the gist box, but the high energy voxels of the 21-grid also
   are high energy in the 41-grid, i.e. in the middle of the grid and far
   the edges of the larger grid.

   I have played around with my trajin settings a bit, reading in only
parts of
   the trajectory, or using only every Nth snapshot, and although I do see
   differences, the same problematic voxels tend to show up again and again.

   As I originally suspected that it could be statistical noise when voxels
   arent populated often enough, I repeated the simulation and wrote out
   snapshots - this even increased the problem. I also tried NVT vs NpT,
to no

   Now my questions:
   1) has anybody else seen this behavior (I have seen one post last year,
   there were no answers) or could there be something wrong with my
   or my analysis (well, this could alwas be the case i suppose) ?

   2) is this normal and expected behavior?

   2) if so, why this happens? Just some weird configuration of one/some of
   snapshots? Numerical instability? A problem of the gist implementation in
   cpptraj? other?

   3) what to do about this? First of all these voxels clutter my
   visualization, but it is also difficult if I want to do some quantitative
   analysis with these grids...can I always expect Eww to be below 0 (I
   no)? Should I try to smooth the grid, e.g. by replacing the high energy
   values by the average of the surrounding 26 voxels?

   Any thoughts or help appreciated!

   PS. Ive run Amber14 pmemd.CUDA, cpptraj version is 15.00, the input file

   trajin cb7_solv.crd
   trajin 1 5000
   autoimage origin
   rmsd CUC :1 first

   gist gridcntr 0. 0. 0. griddim 21 21 21 gridspacn 0.5 out gist_21_05.out

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