Re: SMD working only at high velocity

From: Elia Zumot (
Date: Mon Jul 13 2009 - 10:54:42 CDT

Dear Eric and David,

You are right. After a good nanosecond or so the difference between the
starting and current position becomes obvious, and more so when the spring
constant is bigger, due to the conformational obstacles to the movement of
the substrate through the protein (and there are major changes involved).

My confusion was because of the issue of the Constant velocity which I
assumed to imply that everything else (Force) changes to keep this value
constant at all times (including the beginning of the run).

Thanks a lot


> Elia,
> If your spring constant, "SMDk" is low, you can expect NAMD to move
> the SMD position far before the spring starts pulling hard on your
> atoms. So, at first, it will always look like the atoms are not
> moving; you'll need to wait until SMD has moved several Angstroms to
> verify that your atoms are being pulled along too.
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> David E. Tanner
> Theoretical and Computational Biophysics Group
> 3159 Beckman Institute
> University of Illinois at Urbana-Champaign
> 405 N. Mathews
> Urbana, IL 61801
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> On Jul 10, 2009, at 1:20 PM, Elia Zumot wrote:
> Dear all,
> I'm attempting to move a substrate bound to the protein out of the
> binding
> pocket to see what conformational changes that induces (and major
> changes
> are expected in this case). I'm using SMD with constant velocity for
> that
> with certain harmonic constraints imposed on the protein backbone to
> prevent net translational movement.
> The problem is that the simulation only works at a velocity as 500 A/ns
> but not at the more realistic velocities of 2 or 6 A/ns. This doesn't
> seem
> to make sense (at least not to me) since a lower velocity should mean a
> longer time but not a mere fluctuation of the substrate in its initial
> position (validated by the visualization of the trajectory in VMD and
> the
> position of COM along the direction of applied force).
> Am I missing something here?
> Thanks
> Elia

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:53:02 CST