Hi Marek,
I'm more of a lazy simpleton, but I thought temperature was totally
dependent on velocities, e.g. at the extreme you could wind up a spring
very tight, so it had lots of potential energy, then use normal means to
get it to any temperature you want, maybe even 0 Kelvin?
Bill
On 3/31/19 8:20 PM, Marek Maly wrote:
> Hi Bill,
>
> simply because all the contributions to the energy of the molecule which
> are
> quadratic, contributes as 1/2*k*T
>
> so each contribution to the total energy in the shape like k/2(r-r0)^2
> contributes as 1/2*k*T
>
> see here :
>
> https://en.wikipedia.org/wiki/Equipartition_theorem#Potential_energy_and_harmonic_oscillators
>
> But as I wrote, the easiest way to calculate instantaneous temperature of
> the system composed of complex molecules should be probably to apply
> equipartition theorem just on translational
> part of the kinetic energy. Then we do not need to care about the internal
> structure of molecules. Am I right ?
>
> Best wishes,
>
> Marek
>
>
>
> Dne Mon, 01 Apr 2019 02:57:02 +0200 Bill Ross <ross.cgl.ucsf.edu>
> napsal/-a:
>
>> Why would bond (potential) energy be part of temperature? Asking for a
>> friend. :-)
>>
>> Bill
>>
>> On 3/31/19 5:35 PM, Marek Maly wrote:
>>> Hello,
>>>
>>> I would like to know how exactly the instantaneous temperature is
>>> calculated in Amber.
>>>
>>> I assume that the Equipartition theorem is used but which degrees of
>>> freedom are taken in account in case of more complicated molecules
>>> (flexible models) ?
>>>
>>> Could be possible to describe it more in detail on relatively simple
>>> molecular system composed just of water molecules (flexible molecular
>>> model of course with bond and bond angle harmonic potentials) or
>>> eventually to provide the relavant reference ?
>>>
>>> My guess is, that the averages of kinetic energy <E_kin> or bond energy
>>> (if harmonic approximation is used) <E_bond> or the average of both
>>> energies <E_kin+E_bond> of such molecule could be connected with the
>>> instantaneous temperature using Equipartition theorem this way.
>>>
>>> <E_kin> = 9*0.5*k*T
>>> <E_bond> = 3*0.5*k*T
>>> <E_kin+E_bond> = 12*0.5*k*T
>>>
>>> but I am not sure.
>>>
>>> Thank you in advance,
>>>
>>> Best wishes,
>>>
>>> Marek
>>>
>>>
>>>
>>>
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Received on Sun Mar 31 2019 - 22:00:03 PDT
