Re: Accessing atoms and velocities during NVE run

From: Chris Harrison (
Date: Fri Feb 06 2009 - 12:06:58 CST


You can use tclforces and a "tclforces script" (which you will have to
write) to acquire the coordinates at each step and apply a force to the
atom(s) to modulate the velocity.


Chris Harrison, Ph.D.
Theoretical and Computational Biophysics Group
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave., Urbana, IL 61801                            Voice: 217-244-1733               Fax: 217-244-6078
On Fri, Feb 6, 2009 at 10:57 AM, Nd S <> wrote:
> Dear NAMD users
> I am running a NVE simualtion and after each step I want to modify the
> velocities of of atoms a certain distance apart from the center of the
> cell.  How can I access the velocities and co-ordinates of the atoms after
> each step run and modify them.
> Thanks
> Navdeep

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:52:20 CST