Re: Applying weak harmonic force between two proteins

From: Floris Buelens (floris_buelens_at_yahoo.com)
Date: Thu May 22 2008 - 09:06:57 CDT

There's a straightforward TCL route for defining a center of mass of a group of atoms - see the 'addgroup' command in the 'applied forces and analysis' section of the user's guide. This returns a center of mass that you can apply forces to as if it were a normal atom.
Hope that works for you,

Floris Buelens
Department of Crystallography, Birkbeck College, London

----- Original Message ----
From: "greddy1_at_umd.edu" <greddy1_at_umd.edu>
To: namd-l_at_ks.uiuc.edu
Sent: Wednesday, 21 May, 2008 5:12:18 PM
Subject: namd-l: Applying weak harmonic force between two proteins

Hello all,
I am interested in setting up a dimer simulation. The simulation cell has two
proteins and I am interested in studying how each protein responds to the
presence of the other protein. To efficiently do this I want to apply a weak
harmonic force between the center of mass of the two proteins to prevent them
from flying apart. I can write a detailed Tcl force script (Identifying all the
protein coordinates, calculating the center of mass, then calculating the force
on each and every atom) but I am afraid that it might be very inefficient. Is there
any way to do this succinctly and efficiently using NAMD's inbuilt commands
and functions.
Thank You

G. Reddy
Institute for Physical Science and Technology
University of Maryland, College Park
MD 20742
301-405-9307

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