Re: question about equilibration step

From: Brian Bennion (
Date: Fri Aug 24 2007 - 13:01:07 CDT


One can start with all the Daggett group references. The
equilibration portion of all our simulations to ~2003 (i left after
this) used velocity rescaling to heat the system to the desired
temperature, which is the operationally the same as using a NVT ensemble.

At 09:59 AM 8/24/2007, Richard Wood wrote:
>Hi Peter,
>This is all new to me. All the people I've ever done MD with never
>did this. I wonder where this came from?
>Perhaps you could give us some references, Peter.
>Richard L. Wood, Ph. D.
>University of Minnesota
>Dept. of Medicinal Chemistry,
>College of Pharmacy
>717 Delaware St. SE
>Minneapolis, MN 55414-2959
>----- Original Message ----
>From: Peter Freddolino <>
>To: Richard Wood <>
>Cc: Audrey Salazar <>;
>Sent: Friday, August 24, 2007 12:45:06 PM
>Subject: Re: namd-l: question about equilibration step
>Hi Richard,
> >
> > I don't know why one would want to run an equilibration in NVT and
> > then do your production run in NVE. I would think one would want to
> > be consistent and do the same the whole way through, either use NVE
> > entirely or NVT entirely. The way I look at is is what if one gets
> > unexpected results, then one could ask was it because I used two
> > different ensembles? If one does only use one ensemble, then it's not
> > likely that would be the cause of unexpected results.
>There is at least one very good reason to do this: If you equilibrate
>entirely in NVE, then the only influx of kinetic energy that the system
>gets will be from your velocity initialization. Almost invariably (and
>please do try this), a minimized system will then begin to fluctuate and
>in the process some of this kinetic energy is converted to potential
>energy, causing your temperature to drop. If you equilibrate in this
>way, your energy should be stable almost immediately, but the
>temperature that the simulation is occurring that is much lower than
>physiologically relevant temperatures. If, on the other hand, you
>equilibrate first in NVT, and do so until the temperature is stable, you
>end up with the system at an appropriate temperature *and* with an
>amount of total energy that is appropriate for a system in equilibrium
>with a bath at that temperature. You can then sever the connection to
>the bath and simulate in NVE if you wish, but you will have a more
>realistic initial combination of conformation and velocity distribution.
>Similar logic is why equilibrating in NPT is a good idea even if you're
>going to to production runs in NVT (this is what I frequently do): the
>volume that you initially choose for your system is almost certainly not
>the true volume that it should have at reasonable pressures, and you
>risk having bubbles or regions of abnormal density form in your
>simulation if you don't somehow allow the volume of the system to adjust.
> >
> > As I stated earlier, one generally plots out say the energy of the
> > system as a function of time, and if the curve is relatively flat,
> > then one can say the system is at an equilibrium. I'm not aware of
> > any other way to quantitate whether or not one's system is at equilibrium.
> >
>Please see my email from earlier this morning for some other criteria
>worth looking at.
>Fussy? Opinionated? Impossible to please? Perfect.
>Yahoo!'s user panel and lay it on us.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:09 CST