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From: Carlos Simmerling <carlos.simmerling.gmail.com>

Date: Mon, 1 Apr 2019 07:16:16 -0400

If you go to the amber web page and in the search bar type something like

"how is temperature calculated" you get some useful links to prior

discussions on this. It does indeed use 1/2kT for each dof, subtracting the

number of constraints from the total 3N dof (such as shaken bonds).

On Sun, Mar 31, 2019, 11:20 PM Marek Maly <marek.maly.ujep.cz> 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
*

*> >>
*

*> >>
*

*> >>
*

*> >>
*

*> > _______________________________________________
*

*> > AMBER mailing list
*

*> > AMBER.ambermd.org
*

*> > http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

*>
*

*> --
*

*> Vytvořeno poštovní aplikací Opery: http://www.opera.com/mail/
*

*>
*

*> _______________________________________________
*

*> AMBER mailing list
*

*> AMBER.ambermd.org
*

*> http://lists.ambermd.org/mailman/listinfo/amber
*

*>
*

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Received on Mon Apr 01 2019 - 04:30:03 PDT

Date: Mon, 1 Apr 2019 07:16:16 -0400

If you go to the amber web page and in the search bar type something like

"how is temperature calculated" you get some useful links to prior

discussions on this. It does indeed use 1/2kT for each dof, subtracting the

number of constraints from the total 3N dof (such as shaken bonds).

On Sun, Mar 31, 2019, 11:20 PM Marek Maly <marek.maly.ujep.cz> wrote:

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Received on Mon Apr 01 2019 - 04:30:03 PDT

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