> Just realized that sander actually re-constitutes the excluded list from
> bond, angle, dihedral lists. Any insightful comments why it has to be
done
> this way? What will happen if I disable this (i.e., remove the code)? I
need
> some flexibility in the excluded list but don't like to break too many
> things :(.
Others can elaborate in more precise detail, but as I understand it, the
excluded list or something equivalent is necessary for Ewald calculations
(specifically PME) to correct for overcount of 1-1,1-2,1-3 interactions in
the reciprocal calculation. This "feature" is also extensively used in
LES and path integral MD to exclude interactions of copies with each
other. So, if you are planning on doing accurate simulation with explicit
solvent and PME, I do not think you cannot simply remove this... There
might be a way to replace it or make it more efficient (as Wei has done /
is doing with the PIMD implementation to improve performance considerably
in cases where ALL particles are replicated), but likely this is tricky to
retain the generality of multiple region LES replicas and to avoid lots of
look-up in the nb_adjust routines of PME.
--tec3
Received on Wed Apr 05 2006 - 23:49:50 PDT
