From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Mon Aug 20 2007 - 08:35:02 CDT
Hi Vincent,
this isn't terribly large, and is unlikely to have any averse effects on
his simulation, but using no multiple timestepping on such a system no
discernable energy drift occurs on timescales of tens of nanoseconds
(ie, whatever drift is present is not significant compared to the
expected fluctuations in temperature occuring throughout the
simulation). That's about as close to "perfect" energy conservation as
you're going to get in a simulation, but it can be done, so although a
drift of 4K in 12 ns isn't qualitatively large (and is probably
tolerable for most simulations), you can do a lot better with modest
changes in simulation parameters.
Best,
Peter
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
>>>
>>>
>>>
>>
>>
>>
>
>
>
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