Direction of steered molecular dynamics

From: 周文昌 (wenchangyu2006_at_gmail.com)
Date: Sat Nov 22 2008 - 08:39:51 CST

I want to conduct smd simulation to a system including one substrate and the
pathway for the substrate is not clear. So I want to select a direction for
the force randomly. I can see some messages from old namd manual that I can
change the force based on the velocity of the steered atoms (
http://www.ks.uiuc.edu/Research/namd/2.0/ug/node24.html). But I can not see
any options in namd2.6 manual. I also see some tutorials and we even can
select a proper direction for the force according to the surrounding
structural information of the steered atoms.So can anybody tell me some
smart ways to choose direction for the force acting on the steered atoms?
Thanks.

Best wishes,
Wenchang

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