[gmx-users] Re: energy terms vs. temperature

Dr. Vitaly V. Chaban vvchaban at gmail.com
Wed Sep 7 02:40:10 CEST 2011

Justin, I was speaking only about the bonded (and presumably,
harmonic) potentials. Decreasing the time-step, as I mentioned, never
made the things worse.


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
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> 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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