Re: question about equilibration step

From: Audrey Salazar (
Date: Fri Aug 24 2007 - 09:04:28 CDT

Thank you for your reply. After reading your responses, I have a few
follow-up questions that I am hoping will clarify how best to run the
equilibration in NAMD. I would appreciate any insight that you and/or the
NAMD community might be able to provide

** In the .conf file, does "minimize" work for the equilibration step? What
> ensemble is the minimization performed in? Can I choose it?
> *****************************************************************************
> Generally, one minimizes separately from the equilibration. So, you build
> your system, minimize (actually add energy to it to remove bad contacts,
> etc., and get it into a more "realistic" state, and to familiarize your
> system with the force field) it, and then heat it to your temperature of
> interest. Then, run your equilibration.
> *****************************************************************************

** In other words, I should have a .conf file that I use with the "minimize"
command and a separate .conf file that I run with the "run" command? At
this point let's say that I want to run the equilibration in NVT, I would
specify the temperature using the "temperature" command. Then, if I want to
run the MD in NVE then I would remove the "temperature" command in a
separate conf file?

** Other than letting a simulation equilibrate for a long time, is there
> other NAMD output that I can use to gauge whether equilibrium has been
> reached?
> *****************************************************************************
> One generally looks at the energy or temperature leveling off to some
> "constant" value, which implies that the system has reached equilibrium.
> There will be some fluctuation in the value of the potential; energy, say,
> but if one looks at the "average" value, it should be pretty constant for a
> system that has reached equilibrium.
> *****************************************************************************
I think that in order to have an equilibrated system, I am looking for the
energy to be equally partitioned because it is possible to have a constant
total energy, but have only equilibrated bond stretching energies, but not
bond bending, for example, because the time period required for
equilibration is longer for bond bending. It is possible for the total
energy in the system to remain constant while the bond bending equilibrates
because equal loss and gain of energy from bond stretching to bond bending
would result in no total energy change.

** Am I correct in my understanding? If so, how can I be sure that the
simulation is, in fact, equilibrated? Are there any references that I should
look at?

I hope that I have been clear. Thank you for your help.

Thank you in advance.


Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA

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