scripting in namd

From: Adam Fraser (adam.n.fraser_at_gmail.com)
Date: Wed Oct 31 2007 - 07:39:36 CDT

Hi all,

I'm studying binding/unbinding dynamics of a small system and would like to
repeatedly push and pull the ligand towards and away from the receptor
(preferably by using SMD)

SMD on # Using SMD
SMDFile 2HEX_solv_SMD.pdb # Specify pushed atoms
SMDk 6.6 # spring
const
SMDVel 0.00007 # velocity (A/fs) 20A/300000fs
SMDDir -1 0 0 # xyz force direction
SMDOutputFreq 100 #

My question then, is how can I script the namd config file so that the
SMDDir value alternates between "-1 0 0" and "1 0 0" every X nanoseconds?

Your help is much appreciated,
Adam

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:42 CST