Re: AMBER: Kinetics energy

From: Andreas Svrcek-Seiler <>
Date: Mon, 20 Dec 2004 11:11:10 +0100 (CET)

> 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
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Received on Mon Dec 20 2004 - 10:53:00 PST
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