From: Gungor Ozer (gungor.ozer_at_gmail.com)
Date: Thu Jun 21 2007 - 21:43:03 CDT
Thanks for your reply. That was really useful for me. I am trying to
get PMF at the end of this SMD simulation. And you gave a really good
insight in terms of what was going on there physically.
I am in fact aware of the fact that I would have to get some
deviations but mine is little bit over that "some" amount. I have
already sent a reply explaining the deviations I got in details.
On 6/21/07, Matt Jones <jonesmat_at_physiology.wisc.edu> wrote:
> 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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