From: Ekta Khurana (ekta_at_vitae.cmm.upenn.edu)
Date: Sun May 01 2005 - 16:47:19 CDT
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
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