From: Jonathan Phillips (994phij_at_gmail.com)
Date: Mon Apr 14 2014 - 16:25:04 CDT
I'm a bit confused by the manual (looking at 2.9). Was wondering if
anybody could help clear up my confusion.
The manual says:
"NAMD uses a non-bonded pair list which contained all pairs of atoms for
which non-bonded interactions should be calculated."
This implies that if you have pairlistdist set to anything less than the
box size, true 'full electrostatics' will never be calculated. You'll
calculate PME (if it's on) for every pair of atoms in the pairlist (and
their images in other boxes), but nothing for the atoms which aren't in the
But the default for pairlistdist is cutoff, and the manual says this about
"Next, consider the case where full electrostatics are calculated. In this
case, the electrostatic interactions are not truncated at any distance. In
this scheme, the cutoff parameter has a slightly different meaning for the
electrostatic interactions — it represents the local interaction distance,
or distance within which electrostatic pairs will be directly calculated
This suggests that you can get full electrostatics without setting a
particularly large pairlistdist (or else they'd have mentioned pairlistdist
in that section). Which then suggests that pairlistdist applies only to
short range interactions.
Finally, the manual says:
"PME stands for Particle Mesh Ewald and is an efficient full electrostatics
method for use with periodic boundary conditions."
This suggests that when PME is on, full electrostatics is used, and when
PME is off, it is not used, but that's not explicitly stated.
So are the pair lists referring specifically to short range interactions,
and is my guess right about PME?
Hope you can help,
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