> On Oct 3, 2017, at 2:57 PM, Thomas Pochapsky <pochapsk.brandeis.edu> wrote:
>
> Hi, We are trying to do a force distribution analysis of our solvated
> dynamics tracks (looking for pairwise forces that might help trace out
> mechanical coupling pathways in the protein). We used PME for long
> range interactions, is this likely to introduce errors when looking at
> short range interactions such as adjacent pairwise interactions?
Yes. The short-ranged interactions are damped artificially by a neutralizing Gaussian charge distribution. So it will impact short-range interactions.
The effect of this neutralizing charge distributions is canceled in reciprocal space which is not pairwise decomposable. Ergo there's no straightforward way to pull the contribution of a particular pair interaction from the reciprocal space sum.
> Philosophical suggestions as well as practical ones welcome.
The amount of an interaction that is pushed into reciprocal space depends on Ewald parameters -- e.g. the charge distribution width alpha. The narrower the distribution, the faster the short range interactions are damped and more of it is pushed into reciprocal space.
HTH,
Jason
--
Jason M. Swails
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Received on Tue Oct 03 2017 - 13:00:02 PDT
