From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Aug 19 2007 - 15:53:58 CDT
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.
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,
> 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,
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