From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Fri Aug 24 2007 - 11:59:22 CDT
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
----- 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
> 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.
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