Molecular dynamics simulations

Methods in Molecular Biology

Volumn 443, Issue , 2008, Pages 3-23

  Lindahl, Erik R ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Energy minimization; Equilibration; Force field; Molecular dynamics; Position restraints; Protein; Secondary structure; Simulation; Solvent; Trajectory analysis

Indexed keywords

LYSOZYME; SOLVENT;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; HYDROGEN BOND; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; THEORETICAL MODEL; THERMODYNAMICS;

COMPUTER SIMULATION; HYDROGEN BONDING; MODELS, MOLECULAR; MODELS, THEORETICAL; MURAMIDASE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; SOLVENTS; THERMODYNAMICS;

EID: 84934441543     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-59745-177-2_1     Document Type: Article

References (30)

1. Alder, B.J. and Wainwright, T.E. (1957) Phase transition for a hard sphere system. J. Chem. Phys. 27, 1208-1209.
2. Rahman, A. and Stillinger, F.H. (1971) Molecular dynamics study of liquid water. J. Chem. Phys. 55, 3336-3359.
3. McCammon, J.A. and Karplus, M. (1977) Internal motions of antibody molecules. Nature 268, 765-766.
4. Allen, M.P. and Tildesley, D.J. (1989) Computer Simulation of Liquids. Clarendon Press, New York, NY.
5. Frenkel, D. and Smit, B. (2001) Understanding Molecular Simulation. Academic Press, New York, NY
6. Kaminski, G.A., Friesner, R.A., Tirado-Rives, J., and Jorgensen, W.L. (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J. Phys. Chem. B 105, 6474-6487.
7. MacKerell, A.D. Jr, et al. (1998) All-atom empirical potential for molecular modeling and dynamics Studies of proteins. J. Phys. Chem. B 102, 3586-3616.
8. Oostenbrink, C., Villa, A., Mark, A.E., and van Gunsteren, W.F. (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J. Comput. Chem. 25, 1656-1676.
9. Wang, J., Cieplak, P., and Kollman, P.A. (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J. Comput. Chem. 21, 1049-1074.
10. Chandler, D. (1987) Introduction to Modern Statistical Mechanics. Oxford University Press, New York, NY
11. Essman, U., Perera, L., Berkowitz, M., Darden, T., Lee, H., and Pedersen, L.G. (1995) A smooth particle mesh Ewald method. J. Chem. Phys. 103, 8577-8593.
12. Ryckaert, J.P., Ciccotti, G., and Berendsen, H.J.C. (1977) Numerical integration of the cartesian equations of motion of a system with constraints; molecular dynamics of n-alkanes. J. Comp. Phys. 23, 327-341.
13. Hess, B., Bekker, H., Berendsen, H.J.C., and Fraaije, J.G.E.M. (1998) LINCS: A linear constraint solver for molecular simulation. J. Comput. Chem. 18, 1463-1472.
14. Lindahl, E., Hess, B., and van der Spoel, D. (2001) GROMACS 3.0: A package for molecular simulation and trajectory analysis. J. Mol. Model. 7, 306-317.
15. Case, D.A., et al. (2005) The Amber biomolecular simulation programs. J. Comput. Chem. 26, 1668-1688.
16. Brooks, B.R., et al. (1983) CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. J. Comput. Chem. 4, 187-217.
17. Phillips, J.C., et al. (2005). Scalable molecular dynamics with NAMD. J. Comput. Chem. 26, 1781-1802.
18. DeLano, W.L. (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA. http://www.PyMOL.org.
19. Fleming, A. (1922) On a remarkable bacteriolytic element found in tissues and secretions. Proc. Royal Soe. Ser. B 93, 306-317.
20. Blake, C.C., Koenig, D.F., Mair, G.A., North, A.C., Phillips, D.C., and Sarma, V.R. (1965) Structure of hen egg-white lysozyme. A three-dimensional Fourier synthesis at 2 Angstrom resolution. Nature, 206, 757-761.
21. Rose, D.R., Phipps, J., Michniewicz, J., Birnbaum, G.I., Ahmed, F.R., Muir, A., Anderson, W.F, and Narang, S. (1988) Crystal structure of T4-lysozyme generated from synthetic coding DNA expressed in Escherichia coli. Protein Eng. 2, 277-282.
22. Jorgensen, W.L., Chandrasekhar J., Madura, J.D., Impey, R.W., and Klein, M.L. (1983) Comparison of simple potential functions for simulating liquid water. J. Chem. Phys. 79, 926-935.
23. Berendsen, H.J.C, Postma, J.P.M., and van Gunsteren, W.F. (1981) Interaction models for water in relation to protein hydration, in Intermolecular Forces (Pullman, B., ed.), D. Reidel Publishing Company, Dordrecht, Germany, pp. 331-342.
24. Berendsen, H.J.C., Postma, J.P.M., DiNola, A., and Haak, J.R. (1984) Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81, 3684-3690.
25. Kabsch, W. and Sanders, C. (1983) Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features, Biopolymers 22, 2577-2637.
26. Jorgensen, W.L. and Madura, J.D. (1985) Temperature and size dependence for Monte Carlo simulations of TIP4P water. Mol. Phys. 56, 1381-1392.
27. Mahoney, M.W. and Jorgensen, W.L. (2000). A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions. J. Chem. Phys. 112, 8910-8922.
28. Nosé, S. (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol. Phys. 52, 255-268.
29. Parrinello, M. and Rahman, A. (1981) Polymorphic transitions in single crystals: A new molecular dynamics method. J. Appl. Phys. 52, 7182-7190.
30. Kasson, P., Kelley, N., Singhal, N., Vrjlic, M., Brunger, A., and Pande, VS. (2006) Ensemble molecular dynamics yields submillisecond kinetics and intermediates of membrane fusion. Proc. Natl. Acad. Sci. 103, 11916-11921.