SMD with force applied to two seperate molecules

From: Elia Zumot (
Date: Tue Aug 11 2009 - 10:09:17 CDT

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

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


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