Subject: Re: CCL:MD/MM combination

From: "Ernest Chamot" <[email-masked]>
Date: Tue, 5 Nov 96 18:25:37 EST

Dear Netters:

In his query to the CCL, Rochus Schmid asked:

>What kind of "information" do I get, when performing MD simulations with
>certain parts of the system kept frozen on its position?

And goes on to ask about:

>My conclusion is: at a given temperature (and sufficient sampling) these
>energies form a potential energy surface of the molecule which includes
>temperature and solvent effects "somehow"? But I don't undestand, what kind of
>thermodynamic function this really representates.

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.

EC
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