AMBER Archive (2009)Subject: Re: [AMBER] wrong estimation of hydrogen velocities when using SHAKE?
From: Jose Borreguero (borreguero_at_gmail.com)
Date: Wed Mar 11 2009  13:46:29 CDT
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 XH system.
The kinetic energy of the XH 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, <steinbrt_at_rci.rutgers.edu> 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 HX 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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