From: Vincent Kraeutler (vincent_at_kraeutler.net)
Date: Mon Aug 20 2007 - 02:22:49 CDT
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
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.
> 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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