From: Victor Ovchinnikov (ovchinnv_at_MIT.EDU)
Date: Mon Aug 20 2007 - 08:24:51 CDT
Vincent,
When I set the full electrostatic frequency to 1 instead of 2 at Peter's
suggestion (I had shake on, and was using a 2fs time step), there was no
discernible increase in the temperature or the energy over about 3ns.
Thanks,
Victor
On Mon, 2007-08-20 at 09:22 +0200, Vincent Kraeutler wrote:
> Peter: I'm surprised to see that you consider an energy drift of 4 K
> over 12 ns to be large. Then again, I've never done significant NVE
> simulations. Just out of curiosity: what kind of energy drift would you
> expect?
>
> Cheers,
> v.
>
> Peter Freddolino wrote:
> > Hi Victor,
> > please have a look at the section on integrators in the NAMD paper
> > (Phillips et al., JCC 26:1781--1802, 2005), as these issues are
> > discussed there in some detail. In brief, the Verlet integrator does
> > conserve energy on paper, although there will always be *some* numerical
> > error and very small energy drift (smaller than what you observed) even
> > with a good integrator. As discussed in that paper, the following
> > factors can cause larger energy drift:
> > -Multiple time stepping (anything more aggressive than 1/1/3 for
> > simulations without rigidbonds or 2/2/4 with rigidbonds will not
> > conserve energy well, and 1/1/1 is preferrable)
> > -PME with momentum corrections
> > -any applied forces or constraints (obviously)
> >
> > In practice, NVE simulations with suitable conservative timestepping
> > should show no discernable energy drift. If you do use a thermostat,
> > slightly more efficient timestepping schemes (eg, 1/2/4 for simulations
> > without rigidbonds) can be used. Energy conservation should not (in
> > principle) be affected by SHAKE, although I've never tried this myself.
> >
> > I didn't see a script snippet at the bottom of your email, so I can't
> > comment on the parameters you're using.
> >
> > Best,
> > Peter
> >
> > Victor Ovchinnikov wrote:
> >
> >> Dear all
> >>
> >> I my NVE simulations of a solvated protein system done at 298K (about
> >> 110,000 atoms), the temperature increases by 4 degrees over 12 ns; K.E.
> >> increases by 700 kcal/mol; total energy increases by 2200 kcal/mol;
> >>
> >> a snippet from my script is at the end of this message;
> >>
> >> 1)The integrator used in NAMD is Verlet, which is energy conservative,
> >> correct?
> >> 2)How is the total energy expected to vary in practice?
> >> 3)Is conservation affected by rattle/shake,
> >> 4)Is conservation affected by Timestep splitting?
> >> 5) Which of the script parameters could affect stability the most in
> >> this case (dt, stepspercycle, fullElectFrequency) ?
> >>
> >> Thanks for any feedback,
> >> Victor
> >>
> >>
> >
> >
> >
> >
>
>
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:45:07 CST