molecular simulation references

["Boyd" <boyd@chem.iupui.edu>]

Hello Yanli,

>One of my friend is looking for suggestions on molecular simulation 
>study, he has the follow questions:
>c. any book or good references to this subject? 

Have your friend take a look at the following tutorials, depending what 
his/her specialized interest is.  These chapters are designed to teach 
the newcomer.

T. P. Lybrand, in Reviews in Computational Chemistry, K. B. Lipkowitz 
and D. B. Boyd, Eds., VCH Publishers, New York, 1990, Vol. 1, pp. 295-320.  
Computer Simulation of Biomolecular Systems Using Molecular Dynamics
and Free Energy Perturbation Methods.

J. D. Madura, M. E. Davis, M. K. Gilson, R. C. Wade, B. A. Luty, and J. A. 
McCammon, in Reviews in Computational Chemistry, K. B. Lipkowitz and 
D. B. Boyd, Eds., VCH Publishers, New York, 1994, Vol. 5, pp. 229-267.  
Biological Applications of Electrostatic Calculations and Brownian 
Dynamics Simulations.

K. V. Damodaran and K. M. Merz Jr., in Reviews in Computational 
Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., VCH Publishers, New 
York, 1994, Vol. 5, pp. 269-298.  Computer Simulation of Lipid Systems.

T. P. Straatsma, in Reviews in Computational Chemistry, K. B. Lipkowitz 
and D. B. Boyd, Eds., VCH Publishers, New York, 1996, Vol. 9, pp. 81-127.  
Free Energy by Molecular Simulation.

G. Ravishanker, P. Auffinger, D. R. Langley, B. Jayaram, M. A. Young, 
and D. L. Beveridge, in Reviews in Computational Chemistry, K. B. 
Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1997, Vol. 11, pp. 
317-372.  Treatment of Counterions in Computer Simulations of DNA.

R. Kutteh and T. P. Straatsma, in Reviews in Computational Chemistry, K. 
B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 13, pp. 
75-136.  Molecular Dynamics with General Holonomic Constraints and 
Application To Internal Coordinate Constraints.

J. C. Shelley and D. R. Berard, in Reviews in Computational Chemistry, K. 
B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 13, pp. 
137-205.  Computer Simulation of Water Physisorption at Metal-Water 
Interfaces.

D. W. Brenner, O. A. Shenderova, and D. A. Areshkin, in Reviews in 
Computational Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, 
New York, 1998, Vol. 13, pp. 207-239.  Quantum-Based Analytic 
Interatomic Forces and Materials Simulation.

C. F. Wong, T. Thacher, and H. Rabitz, in Reviews in Computational 
Chemistry, K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 
1998, Vol. 13, pp. 281-326.  Sensitivity Analysis in Biomolecular 
Simulation.

P. Verwer and F. J. J. Leusen, in Reviews in Computational Chemistry, K. 
B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1998, Vol. 13, pp. 
327-365.  Computer Simulation to Predict Possible Crystal Polymorphs.

J. M. Briggs and J. Antosiewicz, in Reviews in Computational Chemistry, 
K. B. Lipkowitz and D. B. Boyd, Eds., Wiley-VCH, New York, 1999, Vol. 13, 
pp. 249-311.  Simulation of pH-dependent Properties of Proteins Using 
Mesoscopic Models.

Best regards, Don
Donald B. Boyd, Ph.D.
Editor, Reviews in Computational Chemistry
	http://chem.iupui.edu/rcc/rcc.html
Editor, Journal of Molecular Graphics and Modelling
	(publication of the ACS COMP division and MGMS)
	http://chem.iupui.edu/~boyd/jmgm.html


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