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

[Justin A. Lemkul]

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 <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
>> 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

========================================