From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Mon Aug 20 2007 - 01:27:14 CDT
Hi,
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.
Regards,
Dave
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.
>
> 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
>>
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