[gmx-users] Re: energy terms vs. temperature
Justin A. Lemkul
jalemkul at vt.edu
Wed Sep 7 02:43:29 CEST 2011
Dr. Vitaly V. Chaban wrote:
> Justin, I was speaking only about the bonded (and presumably,
> harmonic) potentials. Decreasing the time-step, as I mentioned, never
> made the things worse.
How is it that harmonic potentials are unaffected by temperature? Thermal
excitation of bonds is a real phenomenon.
> On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>> Dr. Vitaly V. Chaban wrote:
>>> Hello Juliette:
>>> If you observe such behavior, I would suggest just to decrease a
>>> time-step. You should have the same energies at all temperatures.
>>> The larger is a time-step, the larger is a deviation from the energy
>>> minimum (bonded potentials). The larger is the deviation, the higher
>>> energy/force arises in order to get back to the equilibrium.
>> Shorter time steps may be necessary to maintain stability of the system and
>> to conserve energy, certainly, but I don't understand your point about the
>> energy being independent of temperature. Increasing temperature should, in
>> theory, lead to excited states for bonds so they should be of higher energy.
>> For NVE, temperature fluctuations and compensatory potential changes keep
>> the energy constant, but at different temperatures, NVT and NPT ensembles
>> will inherently have different energies (and techniques like REMD derive
>> their usefulness in part from this fact).
>> A given system should have a constant total energy, but I would certainly
>> expect a system run at 300 K to have a different total energy from one at
>> 400 K.
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
Justin A. Lemkul
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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