From: Boyang Wang (pkuwangboyang_at_yahoo.com.cn)
Date: Sun May 01 2005 - 22:21:46 CDT
If you pull the center of mass, the other atoms will display relative motion with respect to the center of mass more or less.
If you pull a group of atoms right on the edge of the whole group of atmos you are modeling, the whole group may go in one direction. Try to do classical mechanics analysis. I guess the other atoms will vibrate if your force on the center of mass is very small.
You can try to apply the same force to more than one atoms at the end of the group so that the whole group may move in the direction that is to the end you are drawing.
Ekta Khurana <ekta_at_vitae.cmm.upenn.edu> wrote:
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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