Re: [AMBER-Developers] NMR restraints and re-imaging

From: Ross Walker <>
Date: Wed, 8 Nov 2017 15:50:20 -0500

Hi Dan,

Yes this was my understanding as well. The coordinate array is never imaged. A molecule moving out of a box just continues to get larger and larger coordinates. Fractional coordinates are then used in the direct space sum etc to make sure the nearest 'image' molecule is used in the calculation. So I think the question would be if an internal coordinate - say length between the center of mass of two molecules was not strong enough to counter those two molecules moving apart what would happen once they moved more than a box length apart? It depends on if the NMR restraint code is using the absolute coordinates or fractional coordinates. That said in this example would the two molecules not eventually run into their own images?

Note spanning the box with bonds is something we thought about many years ago when simulating cellulose sheets. If one just uses the fractional coordinates in the bond calculation it works although any visualization etc in VMD for example is messed up. I hacked something together in Sander at the time to do this but the problem was it made results highly dependent on box size. The Cellulose sheet would act like a drum skin and vibrate at a frequency that was a function of the box size. So it didn't act as an infinite sheet in the way I naively imagined it would. I also didn't take the time to go through the calculation by hand and figure out if angles and dihedrals were being handled properly at the boundary - or indeed even figuring how they should work in theory. Thus while it would be nice to have this functionality I am not sure how useful it is in practice, it needs thinking about carefully to make sure valence terms aren't being double counted or missed and even if done formally correctly it might mean
 people build what they think are infinite systems but really aren't.

All the best

> On Nov 8, 2017, at 3:37 PM, Daniel Roe <> wrote:
> On Wed, Nov 8, 2017 at 2:46 PM, David Cerutti <> wrote:
>> The current setup re-images all coordinates, molecule by molecule, relative
>> to a single reference frame, then applies the NMR restraints (and any
>> bonded interactions) to those coordinates. Bonds are safe, but if an NMR
>> restraint applies between two separate molecules, there is a slim chance
>> that they will have been re-imaged in a way that suddenly puts an
>> additional box length between them. So the proposed change, which would
> I'm in the middle of an office move today so I don't have time to look
> at this in-depth right now, but I was under the impression that
> sander/pmemd only ever image coordinates for output (not internally).
> This is why a simulation with restraints will work for an initial run
> but sometimes not for the restart. I've got several DNA-stretching
> runs where this was in fact the case, unless the code has been
> significantly modified since then.
> -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 Nov 08 2017 - 13:00:03 PST
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