From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Sun May 01 2005 - 21:23:48 CDT
Hi Ekta,
SMD does not place constraints on the coordinates of the pulled atom(s). It
only adds a force in one direction. The pulled atom(s) still experiences
other forces and can have momentum in any direction. I expect it is possible
to apply harmonic restraints (called constraints in the manual) in the x and
y directions, and to apply SMD forces in the z direction at the same time. I
suspect it would be difficult to constrain the motion of the pulled atom to
a straight line. Why do you want the x and y coordinates to be fixed?
Blake
-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Ekta Khurana
Sent: May 1, 2005 5:47 PM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: SMD-drifting of center of mass
Hello all,
I am using SMD to pull the center of mass of a group of atoms in z
direction with a constant velocity. In the log file the force in
x,y direction is zero as expected and a finite value in the z
direction. However in the trajectory if I see coordinates of the
pulled center of mass, the x,y components are also changing besides
the z component. I tried a more stiff spring (higher force
constant) than what I was using but the problem remains. I tried
force constant value of 250 (in units used by NAMD that is
kcal/mol/angstrom^2). Could anyone suggest why this is happening?
Thanks,
Ekta
--
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:40:43 CST