how does namd handle violations of the minimum image convention?

From: Ana Celia Vila Verde (
Date: Mon Jan 09 2012 - 05:32:32 CST

Hi everyone,

I recently ran (by mistake) a simulation where the cutoff distance was
slightly larger than L/2. I was expecting to get blatantly unphysical
results for violating the minimum image convention, but it turns out
that my protein behaves just fine: results are very similar to
simulations of the same system in which the minimum image convention is
not violated.

Out of curiosity (I don't have any inclination to go about performing
any more simulations like this), can someone explain how namd handles
violations of the minimum image convention, for both PME and VDW?

  I searched the namd-list and found one message indicating that using
rcutoff>L/2 is (numerically) OK for PME because, since with PME we're
calculating full electrostatics anyway, rcutoff simply changes the
distance beyond which electrostatics are calculated using PME. As for
VDW, I'm guessing what happens is that the rcutoff actually becomes L/2
instead of being larger than L/2. Can someone confirm this?



This archive was generated by hypermail 2.1.6 : Mon Dec 31 2012 - 23:21:07 CST