From: Cesar Luis Avila (
Date: Wed Aug 15 2007 - 08:22:59 CDT

Dear all,
I want to calculate non bonded forces (VDW and ELECT) between two groups
of molecules during the course of a simulation. For this I plan to use
NAMD energy plugin, with the exact same parameters used for the
simulation (cutoff, pme). This may be a silly question but, when the
electrostatic forces are calculated, does it take into account the water
in between the molecules? In other words, the forces between the
molecules should be regarded as that on vacuum or in a solvated system?