Re: [AMBER-Developers] Please read: we need to look at pmemd.cuda pair list fidelity

From: Ross Walker <>
Date: Wed, 17 Jan 2018 08:25:28 -0500

Hi Dave,

This is pretty dense so I didn't follow everything. Do you have a simple list of tests that show issues / a 3 line summary of all the issues and the scope of each?

With regards to the very small systems - these have always been problematical and would not be recommended.
That said the code should quit rather than give incorrect answers if one is trying to use a box that is unreasonably small.
Should the limit not be the minimum box dimension needs to be greater than 2 x (cutoff + skinnb)? I believe the default
would be 2.0 for skinnb so in this case 20A making your box too small?

What happens if you run with a 21A box? Do you see those jumps go away? If yes then we may just need a fix here to
limit such tiny boxes. I am assuming the jumps you are referring to are for small systems only?

All the best

> On Jan 16, 2018, at 22:45, David Cerutti <> wrote:
> A lot of study, and posts to a subset of the developers, happened before I
> made this thread on the actual listserv. I was able to make a case, for
> example, where the box volume equilibrates under NPT and we have the
> problem of shrinking hash cells that eventually get too small for the
> cutoff. The problem was fixed for the case of rectangular unit cells, but
> the non-orthorhombic case isn't correctly covered. The simulation settles
> out to a volume where each unit cell is in fact less than the cutoff in
> thickness, irrespective of any pair list margin, but the code thinks it's
> much thicker than therefore keeps right on going. I'll make an NVE case to
> study the energy conservation effects when one of these things happens.
> In the meantime, I've been looking in to the other issue I raised.
> Apologies--I had kept the first issue off of the listserv until I had a
> better idea of what I was seeing, but I fired off the second issue without
> as much discussion. Nonetheless, it seems that there is something going
> on, although it may not quite be what I had thought. The attached plot
> shows the problem. I constructed a cubic box containing 216 TIP3P
> waters--familiar to anyone who's ever tiled such a thing using TIP3PBOX in
> tleap. It's about 18.6A on a side--just big enough to handle an 8A cutoff
> with a 1A margin. Equilibrating and then simulating that in the NVE
> ensemble, I see the energy increase as shown on the attached image. Red
> line = old code. Black line = new code. I need to run it further to
> verify that the new code isn't any more prone to this than the old code,
> but it doesn't appear that may changes to the precision model are doing
> anything detrimental. Furthermore, the occurrence and the size of the
> jumps are random. Something is weird. I've tried various permutations on
> this--pushing the cutoff up to 8.7A with a 0.6A skin, dialing up the
> reciprocal space settings and cutting the time step down to 0.5fs (from
> 1fs) to remove as much noise as possible. I have still seen one of these
> jumps in that situation, but it's too early as of yet to say whether the
> trend has been affected. If I switch to double precision, I can only go
> 1/10th as fast, and I haven't YET seen a jump, but I'm only out to 28ns so
> it might. Some of you may notice that, in between jumps, there is a slight
> DOWNWARD trend to the energy. If the energy isn't flat, errors of any sort
> should drive the energy UP, we thought, but there may be something about
> the fixed precision rounding that imparts an overall tendency to lose
> energy at a very slow rate (not sure on that yet, but the effect is real).
> I tried making a larger box, one which will have three hash cells in any
> direction, and so far I haven't seen any jumps in the energy but there is
> still that slight downward pressure on the overall energy. If I then take
> that larger box and increase the cutoff, so that there are now only 2x2x2
> hash cells once again (but each o them is highly oversized), I am not (yet)
> seeing any jumps of this sort, but that kind of jibes with my original
> hypothesis given what I know about how the pairlist works. You're going to
> see this problem when the box is really small (< 20 thick) and only two
> hash cells thick.
> By tomorrow I'll hopefully have more investigation of the first problem I
> brought up. For now, it looks like I wasn't crying wolf over the second
> one.
> Dave
> On Tue, Jan 16, 2018 at 10:57 AM, Daniel Roe <> wrote:
>> Hi,
>> On Mon, Jan 15, 2018 at 10:11 PM, David Cerutti <>
>> wrote:
>>> What's happening is that, for non-orthogonal unit cells (and the
>>> only case the tleap really knows how to construct is the truncated
>>> octahedron, translating it into a parallelepiped with all angles at
>>> 109.47), sander and pmemd do not know how to properly gauge the distance
>>> between the box faces, and therefore the number of hash cells to create
>>> when building their pair lists.
>> I don't think you are right about this. Sander (and cpptraj and I
>> think pmemd as well) determines the number of grid cells in each
>> dimension using the length of the *reciprocal* cell vectors, which is
>> the inverse of the fractional coordinate system. Because this
>> determination is done in reciprocal (fractional) space, it doesn't
>> matter if the unit cell is orthorhombic or not. All of the "gridding"
>> during the pair list build is also done in fractional space, so I
>> think the pair list builds are fine. Maybe I'm not understanding what
>> you're saying the problem is though. Do you have a specific test case
>> where the pair list is not properly set up (i.e. an atom that is
>> within the cutoff of another atom is skipped)?
>> -Dan
>> --
>> -------------------------
>> Daniel R. Roe
>> Laboratory of Computational Biology
>> National Institutes of Health, NHLBI
>> 5635 Fishers Ln, Rm T900
>> Rockville MD, 20852
>> _______________________________________________
>> AMBER-Developers mailing list
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Received on Wed Jan 17 2018 - 05:30:03 PST
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