From: Cesar Luis Avila (
Date: Wed Aug 15 2007 - 11:15:17 CDT

Hi Peter,
thanks for your fast reply. So, it was as i suspected. How should I
include the solvent in between the molecules on force calculation? It is
difficult for me to figure it out. Should I include the solvent in one
of the two selections? for example
selection1: molecule A
selection 2: molecule B + solvent slice?

For sure, the number of atoms selected will change from frame to frame
in this case. I suppose it will introduce an additional problem when
trying to understand the results.

Thanks again for your help

Peter Freddolino escribió:
> 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