From: Chris Harrison (char_at_ks.uiuc.edu)
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 char_at_ks.uiuc.edu Voice: 217-244-1733 http://www.ks.uiuc.edu/~char Fax: 217-244-6078 On Fri, Feb 6, 2009 at 10:57 AM, Nd S <navdeep79_at_gmail.com> 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 >
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