AMBER Archive (2008)

Subject: AMBER: steered MD initial state

From: M. L. Dodson (
Date: Tue May 06 2008 - 11:04:09 CDT

Hello Ambers,

I have question about setup of SMD runs having to do with selecting
the initial coordinates and velocities. I understand from the
literature that all replicates should be drawn from the same well
equilibrated ensemble. To ensure that I was getting sufficiently
independent trajectories for the SMD replicates, I took my (well
equilibrated) restart file, truncated the velocities with NTX=1, and
set each replicate up with different random number generator seeds
(chosen from output from This is a QMMM run
investigating a proton transfer reaction, so I carried out a 100000
step (0.05fs step size, QM shake turned off) equilibration of the
temperature. Analysis showed the temperature across the trajectory to
have stabilized. I followed this with the SMD run. These SMD
trajectories, differing by random number generator seed, constitute
the replicates to be averaged with the Jarzynski procedure.

Due to a question on the list a couple of days ago, I reread the
Theor. Chem. Acc. paper by Dr. Roitberg and his coworkers. They point
out that the SMD trajectory replicas going into the Jarzynski
averaging algorithm should be drawn from the same starting ensemble.
After rereading the paper, I got nervous. Does my protocol render the
replicate trajectories invalid for use because my protocol means they
are no longer drawn from the same initial ensemble?

My thought process was perhaps too focused on the independence of the
trajectories, but it seems to me this protocol is no more invalid than
repeated experimental atomic force microscope pulling runs.

Does anyone have any comments on this? I would appreciate hearing

Bud Dodson

M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email:	mldodson-at-comcast-dot-net
Phone:	eight_three_two-56_three-386_one
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