Re: question about equilibration step

From: Audrey Salazar (
Date: Fri Aug 24 2007 - 12:22:29 CDT

Good to know about the equilibrating in NPT. That is a good idea to have
both a realistic temperature and volume. From what I understand from these
complicated papers, Langevin temperature control is performed by randomly
selecting a particle and changing its velocity (both magnitude and
direction) leads to problems with momentum conservation. This is a problem
always in MD, but it is accentuated more in Langevin and Berensen (which i
think is an off-shoot of Langevin) than in Nose-Hoover thermostats. I am
not disputing that its use still gives applicable, physical results, just
that relaxation times could be off and this is something that I will care
about in my simulations. This leads to a few questions that I will mark
with **

** I have had much harder time coming up with good references to understand
the Nose-Hoover Langevin piston. Any recommendations? Can I draw analogies
from the Nose-Hoover thermostat?

** I know that the type of temperature control used in equilibration doesn't
appreciably affect the finding equilibrium. Am I right in assuming that
they barostat will also not affect equilibration?

** Is there a way to employ a Nose-Hoover thermostat in NAMD? Is the same as
the temperature coupling mentioned here:

Thank you much.



On 8/24/07, Peter Freddolino <> wrote:
> 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

Audrey L. Salazar
Amaral Research Group
Dept. of Chemical and Biological Engineering      Phone: 847.491.2188
Northwestern University
Evanston, IL USA

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:09 CST