Re: question about equilibration step

From: Neema Salimi (
Date: Fri Aug 24 2007 - 14:32:17 CDT

Yeah, the difference is huge if you don't equilibrate NVT or NPT
before switching to NVE. Another trick is not to over-minimize the
system, since that will lead to longer equilibration times (i.e. you
have to pump thermal energy in longer because you reduced the
potential energy too much to start with). For a well-resolved
crystal structure (e.g. < 1.8 A, no missing coordinates), this could
be as short as 100 cycles of minimization in preparation for a 300K

On Aug 24, 2007, at 11:01 AM, Brian Bennion wrote:

> Hello,
> 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.
> Brian
> 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
>> 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
>> Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s
>> user panel and lay it on us.

Neema Salimi

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
Lab Phone: (415) 476-5143

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