RE: regarding constant velocity steered molecular dynamics

From: Radak, Brian K (
Date: Wed Feb 08 2017 - 11:48:09 CST

Only the pulling velocity is constant - there are other (possibly stochastic) forces on your system that will result in decidedly not constant velocities being added to your pulling velocity.

That being said, there still could be something weird here. I also have no idea what freezing part of the system will do (I'm not sure this is the same thing as a constraint in NAMD, it depends on how the forces are handled and what the coordinates are).


Brian Radak
Postdoctoral Appointee
Leadership Computing Facility
Argonne National Laboratory

9700 South Cass Avenue, Bldg. 240
Argonne, IL 60439-4854
(630) 252-8643
From: [] on behalf of mrinal patel []
Sent: Wednesday, February 08, 2017 4:07 AM
Subject: namd-l: regarding constant velocity steered molecular dynamics

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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