[AMBER] How the instantaneous temperature is calculated in Amber ?

From: Marek Maly <marek.maly.ujep.cz>
Date: Mon, 01 Apr 2019 02:35:05 +0200


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,


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Received on Sun Mar 31 2019 - 18:00:02 PDT
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