Re: question about equilibration step

From: Richard Wood (
Date: Fri Aug 24 2007 - 11:22:01 CDT

Hi Audrey, 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. I think if the energy is fairly "constant" in an equilibrated system, then there won't be fluctuations among the various components because it's equilibrated. If there are fluctuations in various parts of the energy, then chances are your system isn't equilibrated, and the total energy isn't really "constant". I know my argument is kind of circular, but that is how it works. I also don't know how there could be large fluctuations in bond bending or stretching and yet, have the system be at equilibrium. 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. If I am wrong, I'm sure someone out there in MD land will correct me. 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: Audrey Salazar <> To: Richard Wood <>; Sent: Friday, August 24, 2007 10:04:28 AM Subject: Re: namd-l: question about equilibration step Hello, 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 -- Audrey L. Salazar Amaral Research Group Dept. of Chemical and Biological Engineering Phone: 847.491.2188 Northwestern University Evanston, IL USA ____________________________________________________________________________________ Luggage? GPS? Comic books? Check out fitting gifts for grads at Yahoo! Search

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