Code question: Partitioning the patch contents into water and non-water

From: Vincent Kraeutler (
Date: Fri Aug 17 2007 - 04:01:24 CDT


I'm currently looking into customized water-water interactions. So one
thing I need to do is to partition the atoms contained in a patch into
water and non-water. From what I can tell so far, this seems to be
non-trivial, i.e. it looks like the atoms contained in a given patch
come in no particular order.

I would be deeply grateful if anyone could answer the following questions:

i) Are the atoms in a patch sorted in any particular way? (I think they
are not, but I'm not sure). If so, which one?

ii) If I need to sort the atoms, I suppose it would be best to perform
the sort right after atom migration and before the assignment to compute
objects. Could you suggest where (in the code) I would best do that?
(I'm currently looking at PatchMgr.* and friends with limited success)

iii) How would I go about distinguishing water from non-water atoms? Or
even just solvent from solute atoms? Is there an explicit way to do it,
or would I have to go via topological information?

Thanks & cheers,

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