Re: CCL:MD/MM combination

 > 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
 > system is frozen, should those atoms be included in the
 > 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
 > any answer to Rochus's question can also answer my question.  Thanks.
 	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 Kerdcharoen, Ph.D.
 Profession:   Lecturer and Information Technology Consultant
 Address:      Department of Physics, Mahidol University, Bangkok 10400
 Phone:        2461381  FAX  2461381
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