AMBER Archive (2008)

Subject: Re: AMBER: steered MD initial state

From: Adrian Roitberg (
Date: Tue May 06 2008 - 12:16:52 CDT

Gustavo is basically right.
The main issue is your comment of "I took my (well
equilibrated) restart file". There is not such thing as a single set of
coordinates being well equilibrated.
In fact, a single set of coordinates belongs to an infinite number of
ensembles, with different weights, which, being a single set, are not

If one wants to run many free MDs, then starting from one set of
coordinates with many different random velocities is ok, since given
infinite time they will all 'equilibrate' to the proper ensemble. For
SMD/Jarzynski, you need different set of coordinates compatible with the
initial restraint.

So, as Gustavo said, pick a number of snapshots from the initial
restrained MD, and start SMD from each one.

Hope this helps.


Gustavo Seabra wrote:
> Hi Bud,
> If I understood correctly, what you are getting are maybe different
> trajectories, but all started from the same replica, that only differ
> on the random number used as seed. After the temperature
> equilibration, You end up with a number of different restart files
> which you then use for the SMD runs, is that correct? If this is the
> case, I'm afraid you may be right and the different starting points
> are not necessarily of the same ensemble.
> The idea in Jarzynski calculations is that each replica will be a
> different *starting point* for the process, all belonging to the same
> initial ensemble. The way we do it here is extracting frames from an
> equilibrated trajectory, for example, one frame every 100ps or so, so
> that each replica is a different starting point, all belonging to this
> same initial ensemble. Still, it is a good idea to give each replica a
> different random number seed, especially if you are using the Langevin
> thermostat (which you SHOULD, especially for QM/MM calculations).
> HTH,
> Gustavo.
> On Tue, May 6, 2008 at 12:04 PM, M. L. Dodson
> <> wrote:
>> 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
>> them.
>> 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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                            Dr. Adrian E. Roitberg
                              Associate Professor
               Quantum Theory Project and Department of Chemistry

University of Florida PHONE 352 392-6972 P.O. Box 118435 FAX 352 392-8722 Gainesville, FL 32611-8435 Email ============================================================================

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