AMBER Archive (2004)

Subject: Re: AMBER: Kinetics energy

From: Andreas Svrcek-Seiler (svrci_at_tbi.univie.ac.at)
Date: Mon Dec 20 2004 - 04:11:10 CST

Hi,
> I like to know why Ekin in sander MD seems to be very higher than RT. (is
> Ekin in Kcal/mol, isn?t it?).
Like every degree of freedom (DOF) (which enters the hamiltonian purely
quadratically), it should -on average- be kT/2 (or RT/2) per DOF or 3
N_atoms /(2 kT) for N_atoms atoms and no constraints (be it on bonds or center of mass
motion). I hope this helps.
good luck
Andreas
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