From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Aug 24 2007 - 12:25:03 CDT
please have a look, for example, at
Marcos Sotomayor, David P. Corey, and Klaus Schulten. /Structure/,
or the charmm tutorial at
or, for example, the amber mailing list archives at
More to the point, please just try it yourself. Take a structure,
solvate it, minimize it, initialize, the velocities, and run some NVE
simulations, and plot the resulting temperature. You'll probably see a
major drop in temperature, which should raise questions about how
realistic the conditions of your simulation are.
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 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 <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
> Please see my email from earlier this morning for some other criteria
> worth looking at.
> Fussy? Opinionated? Impossible to please? Perfect. Join Yahoo!'s user
> and lay it on us.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:09 CST