Re: question about equilibration step

From: Neema Salimi (nsalimi_at_msg.ucsf.edu)
Date: Fri Aug 24 2007 - 14:59:19 CDT

Anyone who cares about the MD kinetics is doing NVE, as the NVT/NPT
will perturb the kinetics. And if you're struggling with the concept
of an "energy bath," how about considering an isolated system, where
no energy or particles are exchanged between the system and the
environment. Note, this isn't just a closed system, because at
constant V, we can't do PV work either.

(resending, forgot to reply all)

On Aug 24, 2007, at 12:45 PM, Richard Wood wrote:

> Hi all,
>
> Again, I ask what groups are doing NVE simulations? My experience
> is that most people do NVT/NVT (I'm struggling with the concept of
> an "energy bath" in my mind...)
>
> Richard
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55414-2959
> rwoodphd_at_yahoo.com
>
>
>
>
>
>
> ----- Original Message ----
> From: Neema Salimi <nsalimi_at_msg.ucsf.edu>
> To: Brian Bennion <bennion1_at_llnl.gov>
> Cc: Richard Wood <rwoodphd_at_yahoo.com>; Peter Freddolino
> <petefred_at_ks.uiuc.edu>; Audrey Salazar
> <alsalazar_at_northwestern.edu>; namd-l_at_ks.uiuc.edu
> Sent: Friday, August 24, 2007 3:32:17 PM
> Subject: Re: namd-l: question about equilibration step
>
> 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 simulation.
>
> 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
>>> rwoodphd_at_yahoo.com
>>>
>>>
>>> ----- Original Message ----
>>> From: Peter Freddolino <petefred_at_ks.uiuc.edu>
>>> To: Richard Wood <rwoodphd_at_yahoo.com>
>>> Cc: Audrey Salazar <alsalazar_at_northwestern.edu>; namd-l_at_ks.uiuc.edu
>>> 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
> nsalimi_at_msg.ucsf.edu
>
> University of California-San Francisco
> Graduate Group in Biophysics
> Agard Lab
> http://msg.ucsf.edu/agard/
> Lab Phone: (415) 476-5143
>
>
>
> Moody friends. Drama queens. Your life? Nope! - their life, your
> story.
> Play Sims Stories at Yahoo! Games.

Neema Salimi
nsalimi_at_msg.ucsf.edu

University of California-San Francisco
Graduate Group in Biophysics
Agard Lab
http://msg.ucsf.edu/agard/
Lab Phone: (415) 476-5143

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