RE: SMD-drifting of center of mass

From: Blake Charlebois (
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?


-----Original Message-----
From: [] On Behalf
Of Ekta Khurana
Sent: May 1, 2005 5:47 PM
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?


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