Re: SMD with force applied to two seperate molecules

From: Elia Zumot (
Date: Thu Aug 13 2009 - 11:07:06 CDT

Hi Roman,

In principle it shouldn't matter whether I'm using CV or CF since both
rely on using a single reference file to specify which atoms are to be
moved and which to be constrianed.

I'm pulling both substrates in the same direction because that way I will
get two results for every run (statisically more significant and so will
need less runs).
The problem arises when one substrates starts moving before the other
(succeeds in crossing the energy barrier first) because if it is a single
COM point in space for both substrates then you will start getting

Any help from the original NAMD programmers on the issue of COM?

Thanks for the responses.


> to my understanding imaginary SMD point is the COM of the group of all
> SMD-atoms.
> 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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