Re: SMD with force applied to two seperate molecules

From: Roman Petrenko (
Date: Thu Aug 13 2009 - 10:24:02 CDT

to my understanding imaginary SMD point is the COM of the group of all

why do you need to apply a force to both molecules? fix one and move the other.

if you indeed need to pull two molecules, each in opposite direction,
the only solution is to use tcl-forces script (not for beginners).

On Tue, Aug 11, 2009 at 11:09 AM, Elia Zumot<> wrote:
> Dear NAMD users,
> I'm doing SMD with CV for a dimer protein (each has its own substrate) by
> applying force to the two substrates (about 20 A apart, using a single
> reference file) to force them out of their binding pocket.
> I got two questions:
> 1)Is the COM (where force is applied) in this case an imaginary point in
> space halfway between the two molecules or are there two COMs?
> 2) Is it possible to get the trajectory of Force (or PMF) applied to each
> molecule alone? (or alternatively apply two different forces to both
> substrates)
> I am also asking this because only one of the two molecules moves but not
> the other (whereas at higher unrealistic velocities both move).
> Thanks in advance
> Elia

Roman Petrenko
Physics Department
University of Cincinnati

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