Hello,
Hopefully adding to the discussion, here's a bunch of information that may
help now or in the future:
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?
>
values up to 1E19, and about 13000 of the 68921 data points have a Eww-norm
> > 100 kcal/mol.
>
These values are strange...I haven't seen anything like them before
personally. Eww-norm is the average per water solvent-solvent energy and
should roughly relate to bulk water energy, which depending on the model in
use is somewhere between -9 and -11. That being said as water interacts
with a solute Eww can approach 0, or positive, as Esw becomes more negative
(I'm just stating a general trend here, it in no way reflects all possible
scenarios, but may be helpful in thinking about solvent energies in the
future). Outright positive Eww values are possible, but certainly abnormal
(this would be an interesting phenomena if the values weren't so large).
so there might be some edge/PBC effects
> (really??),
>
GIST energy is calculated using the parameters defined in your prmtop,
provided the system was flagged as containing boundary conditions there
should be no issue here.
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?
Frankly those large positive energies are likely due to collisions,
especially the 1E19 values. If so perhaps the autoimaging/ aligning steps
are somehow placing waters on top of each other? I suppose one way to check
this is to plot the system energy before and after aligning to see if that
somehow skews energy.
All other answers thus far appear to be related to autoimaging, restraints,
and the like so this appears to be the consensus.
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?
Aside from tracking down the cause of the energies you can smooth the grid
as you stated, you can also see (shameless plug)
http://ambermd.org/tutorials/advanced/tutorial25/section4.htm. GISTPP (Gist
post processing) can be used to remove the voxels that contain abnormal
energies by using the clear 1 function...something like this:
./gistpp -i Eww-norm.dx -op clear1 -opt cutoff1 100 -opt lt1 -o
nothinglargerthan100.dx
./gistpp -i nothinglargerthan100.dx -i2 Eww-norm.dx -op mult -o
Eww-norm-lt100.dx
This would map only voxels that don't have excessively high energy as what
we call a binary file (1 for voxels that you want, 0 for voxels you don't)
and then multiplying that back into Eww-norm to map Eww values that are of
interest (in this case non-excessive).
In general I would be interested to know if the Esw-norm values in those
same voxels are also abnormally high, just out of curiosity.
Hopefully this information adds to/ helps the situation. On a side note if
after considering imaging and restraints the issue persists I'd be happy to
investigate the issue more thoroughly.
Best of luck,
--Steven Ramsey
PhD Student Lehman College, Kurtzman Lab
On Mon, Aug 10, 2015 at 5:49 AM, Thomas Fox <thomas_fox.gmx.net> 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 cb7_solv.top
> trajin cb7_solv.crd
> trajin prod.traj.nc 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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>
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Received on Mon Aug 10 2015 - 10:00:02 PDT
