question regarding nearest-image resolution in NAMD

From: Vincent Kraeutler (
Date: Mon Sep 03 2007 - 03:23:24 CDT

Dear NAMD list,

I am having a hard time understanding the implementation details of
nearest- (periodic-) image resolution in NAMD, and would appreciate any
helpful advice.

I could observe that:

-- in the ComputeNonbondedPair objects, the positions of the atoms
(located in the primary patch) are periodicity-resolved, i.e. the atoms
in the primary patch satisfy the nearest-image criterion with respect to
the atoms in the secondary patch;

-- in the HomePatch objects, where most of the patch migration seems to
be managed, all atoms seem to be located in the central box. At least
they are different (by a box edge shift) from the ones in the
ComputeNonbondedPair objects.

Somewhere in between, perdiodicity resolution seems to take place. It
seems that Lattice objects are responsible for (or at least involved in)
performing periodicity resolution, but I am having difficulties seeing
the link between ComputeNonbondedPair and Lattice objects, where I
suppose the resolution should take place.

Help is greatly appreciated.

Kind regards,

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