From: David Tanner (guacamoleo_at_gmail.com)
Date: Fri Jul 10 2009 - 15:12:06 CDT
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
http://www.linkedin.com/in/davidetanner
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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
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