regarding constant velocity steered molecular dynamics

From: mrinal patel (
Date: Wed Feb 08 2017 - 04:07:24 CST

I am running a constant velocity SMD simulation on a protein molecule using
NAMD. In the simulation I have constrained a portion of molecule to remain
fixed while I am pulling another portion with a constant velocity.
What I see in the visualization is that for a long time the portion I am
pulling does not move at all while after some time it suddenly moves.
My doubt is if I am constraining some chunk of atoms in a molecule to move
with constant velocity why is it not moving for some time and then suddenly
it moves??
As per the rule of kinematics if a body is constrained to move with a
constant velocity (whose magnitude is not zero) it should move irrespective
of the conditions. I would be grateful if someone helps.

Mrinal Patel

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