[gmx-developers] Non-periodic interaction in a periodic box

Berk Hess hess at kth.se
Thu Aug 21 09:11:32 CEST 2014


But there is another issue here. With domain decomposition different 
parts of the molecules are on different MPI ranks, so you will have to 
decide where to calculate the interaction and do extra communication (in 
general), since the molecule is probably larger than the cut-off distance.

The pull code solves both issues by calculate the COMs using so-called 
"pbc" atoms. The distance for each COM is determined, with pbc, relative 
to a chosen "pbc" atom. The COM is then the coordinate of the pbc atom 
plus the COM distance from this atom. All ranks then do the, identical, 
pull force calculation. But this only works, relatively, efficiently 
when there are few pull coordinates.
If you have few of those interactions, you could use a similar 
mechanism, but that will require some coding.



On 08/20/2014 05:21 PM, David van der Spoel wrote:
> Hi,
> I wonder whether it is possible to define special interactions, say 
> between all atom-pairs in a protein, not considering PBC. That is, to 
> have a box which is slightly larger than the protein but not twice as 
> large in all dimensions, and define these special interactions without 
> considering PBC. This then assumes that the molecule is non-periodic 
> itself.
> Previously this would have been possible using the graph mechanism, 
> but with domain decomposition molecules are split into atoms when they 
> move over the box boundary, right?
> An ugly way could be to restrain the protein in the center of the box 
> and ignoring PBC for the special interactions, but this would not 
> conserve energy, and be dependent on the location of the protein which 
> one can not be sure of when computing the interaction.

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