AMBER Archive (2009)

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

From: steinbrt_at_rci.rutgers.edu
Date: Wed Mar 11 2009 - 12:45:56 CDT

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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