Re: question about equilibration step

From: Richard Wood (
Date: Fri Aug 24 2007 - 11:59:22 CDT

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 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. Best, Peter ____________________________________________________________________________________ Got a little couch potato? Check out fun summer activities for kids.

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