Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE?

From: Jose Borreguero <>
Date: Wed, 11 Mar 2009 14:46:29 -0400

Dear Thomas,

Your assumption is correct: (3/2)kT for the X atom and (2/2)kT for the H
atom makes a total of (5/2)kT for the X-H system.
The kinetic energy of the X-H system is still the sum of the kinetic
energies of each atom, no matter which constraints you decide to impose.

On Wed, Mar 11, 2009 at 1:45 PM, <> wrote:

> Hi Jose,
> > I assume that since SHAKE reduces the number of degrees of freedom by one
> > due to the constrain, then maybe for hydrogens Ek=kT instead of (3/2)kT.
> I
> > computed Ek for each hydrogen in the simulation with SHAKE, and using
> > Ek=kT
> > I got T about 6% higher than system temperature. Pretty close.
> are you certain that that is a valid breakdown of the systems degrees of
> freedom? The SHAKE constraint doesn't neatly remove one DOF from the
> hydrogen, but it also couples its movement to that of the bound heavy
> atom. I would have assumed that, in such a constrained system, only the
> kinetic energy of the combined H-X system would be meaningful (and 5/2 kT
> for three translational and two rotational degrees of freedom) but I'm far
> from certain about it.
> Kind Regards,
> Thomas
> Dr. Thomas Steinbrecher
> BioMaps Institute
> Rutgers University
> 610 Taylor Rd.
> Piscataway, NJ 08854
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Received on Fri Mar 13 2009 - 01:13:16 PDT
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