Re: SMD atoms are not moving in accordance with steering parameters!

From: Matt Jones (
Date: Thu Jun 21 2007 - 02:28:03 CDT

Hi Gungor,

This is my first time posting to the namd-l list, so just in case it
doesn't work I'm also responding to you directly by email.

I'm not an expert, but recently did some SMD also. So here's my
potential explanation (pun intended, see below).

You are not necessarily doing anything wrong.

I think you _shouldn't_ expect the steered atoms to move along
exactly the same trajectory or velocity as you specified. What SMD is
doing is creating a "virtual atom" that is moving along the vector
and velocity that you specify. This is not the "steered atom", but is
attached to the steered atom by a "virtual spring". Imagine attaching
two tennis balls together with a slinky, and pulling one (the virtual
atom) by hand as you walk along, while the other one (the steered
atom) bobs along in the grass behind you. Depending on the contours
and bumps of the ground that the steered ball experiences (i.e., the
protein, lipid or water environment), it will curve and bounce, and
the springy slinky will stretch and contract, even if the ball in
your hand is moving in a straight line with constant velocity.
Therefore the steered ball won't follow the same vector, but will
take a path that is some energy-minimizing combination of the
displacement vector of your steering ball and the force vectors due
to the local environment that it is in (e.g., bumps on the ground,
molehills, etc).

Indeed, one can infer useful things about the local environment by
analyzing the deviations from the steering vector, and the changes in
length or force of the spring. For example, if there are particular
locations where the steered atom lags far behind the spring, or
spends a lot of time before moving on, this suggests an energy
barrier (a bump on the lawn) at that location. Eventually, the
stretching of the spring may apply enough force to overcome the
barrier, and the steered atom will then surge forward. The difference
in positions and velocities between the steering atom and steered
atom are directly related to the height and structure of the energy
barrier, etc. This is the basis of using SMD to compute the Potential
of Mean Force (PMF), which is an estimate of the local energy landscape.

Makes sense?

Might not make sense, because as I said, I am no expert. Someone else
please correct any errors in my explanation!


Matt Jones

On Jun 20, 2007, at 10:35 PM, Gungor Ozer wrote:

> Hello all,
> I have been trying to run a Steered MD simulation on a small peptide.
> What I've been doing is basically pulling a whole residue at a
> realtively appropriate velocity (10^-4 orders of magnitude of
> A/timestep) in a box full of TIP3 water molecules at 500K. The
> aminoacid is not a part of a beta strand or an alpha helix and its
> only non-bonded interactions are those with waters.
> The problem I am facing is simply that my steered residue was not
> moving along the direction vector and velocity I have been assigning.
> Does anybody know what I might be doing wrong? Or, has anybody
> experienced similar problems? And finally, do you have any potential
> explanation (or solution) to this issue?
> Thank you all in advance...
> --
> -gungor

Mathew Jones
Department of Physiology
University of Wisconsin-Madison
283 MSC
1300 University Ave
Madison, WI 53706

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