From: Elia Zumot (enz1+_at_pitt.edu)
Date: Fri Jul 10 2009 - 13:20:33 CDT
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?
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