Molecular modeling References

Force Fields

AMBER 94

Wendy D. Cornell, Piotr Cieplak, Christopher I. Bayly, Ian R. Gould, Kenneth M. Merz, Jr., David M. Ferguson, David C. Spellmeyer, Thomas Fox, James W. Caldwell, and Peter A. Kollman (1995)
"A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules"
J. Am. Chem. Soc., v.117, pp.5179-5197

OPLS

William L. Jorgensen and Julian Tirado-Rives (1988)
"The OPLS Potential Functions for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin"
J. Am. Chem. Soc., v.110, No.6, pp.1657-1666

Flexible SPC water model

K. Toukan and A. Rahman (1985)
"Molecular-dynamics study of atomic motions in water".
Physical Review B 31: 2643-2648. doi:10.1103/PhysRevB.31.2643

At Wikipedia

Thermostats

At SklogWiki

Andersen

Hans C. Andersen
"Molecular dynamics simulations at constant pressure and/or temperature",
Journal of Chemical Physics v.72 pp.2384-2393 (1980)

Lowe-Andersen

C. P. Lowe (1999)
"An alternative approach to dissipative particle dynamics",
Europhysics Letters v.47 pp. 145-151

E. A. Koopman and C. P. Lowe (2006)
"Advantages of a Lowe-Andersen thermostat in molecular dynamics simulations"
Journal of Chemical Physics v.124 204103

Berendsen

H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. DiNola, and J. R. Haak (1984)
"Molecular dynamics with coupling to an external bath"
Journal of Chemical Physics v.81 pp. 3684-3690