AMBER Archive (2008)

Subject: Re: AMBER: steered MD initial state

From: M. L. Dodson (
Date: Tue May 06 2008 - 12:39:04 CDT

Adrian Roitberg wrote:
> Bud,
> 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
> available.

Yeah, I understand that. I should have said I took a single (the
last) frame from a well equilibrated trajectory. But the point you
make is well taken.

See my reply to Gustavo for the explanation of why I did it the way I
did. If what I have done is meaningless, I will certainly toss it and
proceed again along the way you and he describe. I still have a
little problem reconciling in my mind how we do it in a simulation
with the way the experimentalists set things up, although it is
beginning to penetrate a little bit ;-)

> 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.
> Adrian

> 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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