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

From: Marek Maly <>
Date: Mon, 01 Apr 2019 05:02:36 +0200

Maybe the easiest way could be to work just with translational degrees of
freedom i.e. to use just the translational part of kinetic energy of
whole molecules and relate it to the temperature like this:

E_kin_translational_total = N*3/2*k*T

where N is the number of molecules or

E_kin_translational_total = (N-3)*3/2*k*T

if the total momentum is fixed.

This way we do not need to care about the internal degrees of freedom of
the individual molecules.

  Am I right ?

     Best wishes,


Dne Mon, 01 Apr 2019 02:35:05 +0200 Marek Maly <>

> 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 - 20:30:02 PDT
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