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 - 18:00:02 PDT
