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From: Marek Maly <marek.maly.ujep.cz>

Date: Mon, 01 Apr 2019 02:35:05 +0200

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

Date: Mon, 01 Apr 2019 02:35:05 +0200

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

-- Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/ _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sun Mar 31 2019 - 18:00:02 PDT

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