Re: [AMBER] cpptraj gist: Eww energies

From: Nguyen, Crystal <>
Date: Mon, 10 Aug 2015 15:42:30 +0000

Hi Thomas

Thanks for bringing this problem up. Did you restrain the cucurbituril during your simulation? We have seen this problem in the past with unrestraint simulation when trying to do rms fit and autoimage command before running gist. The rms fit aligns the solute but does not modify the box or the unit cell vector so it could destroy the imaging.

Hope it helps.


> On Aug 10, 2015, at 2:50 AM, Thomas Fox <> wrote:
> Hi,
> I started playing around with the gist functionality in cpptraj and thought
> 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 in
> total 5000 snapshots, I get plots that look very similar to what Nguyen et
> al report in their paper.
> However, when looking at the Eww-norm.dx data, I see a number of voxels that
> 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 for
> 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.
> My simulation box is about 35x35x35A, i.e. for larger gist grids one comes
> 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 from
> 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 some
> 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 250000
> snapshots - this even increased the problem. I also tried NVT vs NpT, to no
> avail.
> Now my questions:
> 1) has anybody else seen this behavior (I have seen one post last year, but
> there were no answers) or could there be something wrong with my simulation
> 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 the
> 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 suspect
> 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!
> Th.
> PS. Ive run Amber14 pmemd.CUDA, cpptraj version is 15.00, the input file is
> parm
> 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
> run
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Received on Mon Aug 10 2015 - 09:00:02 PDT
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