From noy -x- at -x- einstein.sc.mahidol.ac.th  Wed Nov  6 09:19:37 1996
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From: "Dr. Teerakiat Kerdcharoen" <noy #at# einstein.sc.mahidol.ac.th>
Message-Id: <199611070352.UAA32384.,at,.einstein.sc.mahidol.ac.th>
Subject: Re: CCL:MD/MM combination
To: chemistry- at -www.ccl.net
Date: Wed, 6 Nov 1996 20:52:51 -0700 (GMT+7)
In-Reply-To: <echamot.1197623977B |-at-| quake.xnet.com> from "Ernest Chamot" at Nov 5, 96 06:25:37 pm
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> Now I have a question.  What "temperature" is this type of MD going to
> simulate?  Temperature normally just reflects the average kinetic energy of
> the system, so it can be calculated from the velocities.  But if part of the
> system is frozen, should those atoms be included in the "average"? 
> Obviously, if all atoms are included, it will add a bunch of zero
> velocities, so the calculated temperature will be lower than what is
> reflected by the movement of molecules actually allowed to move.  But would
> the "temperature" calculated only by averaging the moving molecules have any
> more meaning?  I suppose that either way this is just an artificial
> situation, but if there is something that corresponds to temperature, I hope
> any answer to Rochus's question can also answer my question.  Thanks.


Hi!
	This point has confined me in a cycle of confusion for quite a
long time. Traditionally, we calculate "temperature" from the ensemble
average of kinetic energy. The kinetic energy is unambiguously defined
as a square of velocity. Well, we assign thermodynamic temperature with
a factor of boltzmann constant and the total degree of freedom of the
system. Things are clear if we consider system as a system of N atoms
moving only translationally and so there are 3N degrees of freedom.
	Things are more ambiguous when people try to devide motions
into 3 modes, translation (of the centre of mass), rotation (about the
C.O.M.) and vibration. Then they introduce the equipartition theorem 
to cope with this. They calculate translational and rotational energies
separately and they have translational and rotational temperature
that are believed to be equal due to the equipartition theorem (frequently
they are much different in some systems that two modes of motion are
not coupled then the macroscopic temperature is calculated by
averaging translational and rotational degrees of freedom). In a system
of rigid molecules, vibration is absent and then the degrees of freedom
from vibration are not employed to calculate temperature.
	In a constraint method, system of rigid molecules can be
consider as a system of flexible molecules with a set of constraint.
For this, only translation motions of N atoms are involved
but the degree of freedom is not 3N, but substracted by an amount
of constraint.
	Your problem may be consider like that, the solute is fixed
with constraint and so not used to calculate temperature.

take care,
Teerakiat

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Teerakiat Kerdcharoen, Ph.D.
Profession:   Lecturer and Information Technology Consultant
Address:      Department of Physics, Mahidol University, Bangkok 10400
Phone:        2461381  FAX  2461381
Cellular:     01-4906089
E-mail:       noy#* at *#einstein.sc.mahidol.ac.th, noy#* at *#atc.atccu.chula.ac.th
Homepage:     http://www.sc.mahidol.ac.th/noy/       
Research:     Computer Aided Molecular Design (CAMD)
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