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.
-Justin
Vitaly
On Tue, Sep 6, 2011 at 7:59 PM, Justin A. Lemkul <[email protected]> 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
--
========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
========================================
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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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