How to apply velocity to the entire system with COMmotion enabled

From: Yinglong Miao (
Date: Mon Sep 29 2008 - 08:43:38 CDT

Dear NAMD users,

I am thinking of a simulation that needs the simulated system moves under an
initial preset velocity. If I turn on the COMmotion and set zeroMomentum to
no, how can I apply the initial velocity to the system COM? As I read the
user guide, SMD seems to work for this. But is it efficient to apply SMD on
all atoms in a big system? And will it cause errors if I use TclBC to apply
boundary conditions along with SMD? Any suggestions will be greatly


Yinglong Miao
Ph.D. Candidate
Center for Cell and Virus Theory
Chemistry Department, Indiana University
800 E Kirkwood Ave Room C203A, Bloomington, IN 47405
Tel: 1-812-856-0981

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