From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Aug 20 2007 - 02:15:11 CDT
thanks for the correction; for some reason I'd thought based on the namd
paper that the zeroMomentum fix lead to energy changes. Learn something
new every day :)
David Hardy wrote:
> A small correction to Peter's comments. Use of zeroMomentum=on will
> correct momentum for PME while still conserving energy. (See preprint
> http://bionum.cs.purdue.edu/SkHP07.pdf for details.)
> Energy drift can also result from incorrect switching/shifting options
> for nonbonded potentials (i.e. config options switching, switchdist,
> and pairlistdist). Generally speaking, a discontinuity in the force
> will cause gradual heating of the system.
> On Aug 19, 2007, at 3:53 PM, 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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