VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Aug 15 2007 - 11:50:55 CDT

Hi Cesar,
this is a good (and important) question. When NAMD calculates pair
interactions, it *only* takes into account the atoms which are members
of the pair interaction selections, so the forces you obtain from it on
the interactions between two sections of solute should be regarded as
the forces in vacuum, and interpreted accordingly. You'd have to include
some section of solvent in your pair interaction calculations to get its
effect included.
Best,
Peter

Cesar Luis Avila wrote:
> 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?
> Regards
> Cesar