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

From: <>
Date: Wed, 11 Mar 2009 14:56:15 -0400 (EDT)

Dear Jose,

> 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.

what I was trying to say is, who tells you that it's the hydrogen that is
constrained? I could also imagine the SHAKE algorithms to constrain the
connected heavy atom's position with respect to that of the freely moving
hydrogen, then it would be 3/2 kT for H and 2/2 kT for X. The reality will
be somewhere in between, with both atoms loosing some kinetic energy. The
sum should always be 5/2 kT, but it is not clear how it is distributed
between the atoms.

>> > I got T about 6% higher than system temperature. Pretty close.

My prediction would be that you will find the 'extra' kinetic energy of
the hydrogens missing from the respective heavy atoms.

Kind Regards,


Dr. Thomas Steinbrecher
BioMaps Institute
Rutgers University
610 Taylor Rd.
Piscataway, NJ 08854

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Received on Fri Mar 13 2009 - 01:13:22 PDT
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