Subject: qustion regarding molecular dynamics simulation

From: [email-masked]
Date: Fri, 27 Aug 93 11:44:07 EDT

Q. How can integration of Newtons eq. of motion can be justified in the 
absence of real solvent molecule while simulating a protein or a dna
motion    motion ? What about friction offered by solvent ?

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From: G. Ravishanker <[email-masked]>
Date: Fri, 27 Aug 1993 08:44:20 -0400

>>   motion    motion ? What about friction offered by solvent ? 

	In the absence of solvent, the model you are studying is usually
the system "in vacuo". This is usually done to check if any unusual
artifacts exist in the force field and used to be the only way one could
study systems in the early days, due to the lack of computational
resources. This therefore has very limited "physical" significance, such
as correlation to experimental data etc. (I am talking about large
biomolecular systems here)

	Solvent can be modelled in several different ways. The extremes
being explicit solvents (TIP4P, SPC are some of the examples) and a simple
continum model using a constant dielectric in the modulation of
electrostatic interaction between the solute atoms. The expense of
computation varies according to the model and is pretty obvious. When
these models are used to solve Newton's equations of motion using the
forces on atoms, it is called Molecular Dynamics.

	The type of model you are interested in, where you want to model
friction of the solvent, you use a different set of equations typically.
These are the stochastic Langevin equations, where in addition to the
forces, a stochastic term to represent the solute-solvent collisions and a
frictional term to express the drag due to solvent appear in the equation.

	Please refer to an excellent review by W.F. van Gunsteren and H.J.C.
Berendsen on all these issues (Angew. Chem. Int. Ed. Engl. v. 29,
992-1023(1990) as well as Allen and Tildesley's book.

Ravi