Abstract
Molecular simulation is a powerful tool in computational physics, with which researchers are enabled to study physical properties of molecular systems at the atomic level. It is therefore of much vitality and one of the most fundamental and effective ways for researchers to study soft-matter physics and biophysics. This chapter majorly focuses on introducing the principles and some applications of molecular modeling and molecular simulation, including Monte Carlo simulation and molecular dynamics simulation. It also presents a synopsis to first-principle calculations, as well as some basic concepts of equilibrium statistical physics that many researchers may find useful. The chapter is collaboratively written by Chenyu Tang (OrcID: 0000-0002-6914-7348) and Prof. Yanting Wang (OrcID: 0000-0002-0474-4790).
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Hohenberg, P., Kohn, W.: Inhomogeneous electron gas. Phys. Rev. 136(3B), 864–871 (1964)
Levy, M.: Universal variational functionals of electron densities, first-order density matrices, and natural spin-orbitals and solution of the v-representability problem. Proc. Natl. Acad. Sci. U.S.A. 76(12), 6062–6065 (1979)
Kohn, W., Sham, L.J.: Self-consistent equations including exchange and correlation effects. Phys. Rev. 140(4A), A1133–A1138 (1965)
Noid, W.G., Liu, P., Wang, Y., Chu, J.W., Ayton, G.S., Izvekov, S., et al.: The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models. J. Chemical Phys. 128 (24), 244115 (2008)
Wang, Y., Noid, W.G., Liu, P., Voth, G.A.: Effective force coarse-graining. Phys. Chem. Chemical Phys. 11(12), 2002–2015 (2009)
Marrink, S.J., Risselada, H.J., Yefimov, S., Tieleman, D.P., De Vries, A.H.: The MARTINI force field: coarse grained model for biomolecular simulations. J. Phys. Chem. B 111(27), 7812–7824 (2007)
Metropolis, N., Rosenbluth, A.W., Rosenbluth, M.N., Teller, A.H., Teller, E.: Equation of state calculations by fast computing machines. J. Chem. Phys. 21(6), 1087–1092 (1953)
Frenkel, D., Smit, B.: Understanding molecular simulation: from algorithms to applications, 2nd edn. Academic Press, Inc. (1996)
Wood, W.W.: Monte Carlo calculations for hard disks in the isothermal-isobaric ensemble. J. Chem. Phys. 48(1), 415–434 (1968)
McDonald, I.R.: NpT-ensemble Monte Carlo calculations for binary liquid mixtures. Mol. Phys. 23(1), 41–58 (2002)
Najafabadi, R., Yip, S.: Observation of finite-temperature brain transformation (f.c.c. → r b.c.c.) in Monte Carlo simulation of iron. Scr. Metall. 17 (10), 1199–204 (1983)
Allen, M.P., Tildesley, D.J.: Computer simulation of liquids, 2nd edn. Oxford University Press (2017)
Berendsen, H.J.C., Gunsteren, W.F.V.: Molecular dynamics simulation of statistical mechanical systems. North Holland Publishing Co Amsterdam (1986)
Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F., Dinola, A., Haak, J.R.: Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81(8), 3684–3690 (1984)
Andersen, H.C.: Molecular dynamics simulations at constant pressure and/or temperature. J. Chem. Phys. 72(4), 2384–2393 (1980)
Hoover, W.G.: Constant-pressure equations of motion. Phys. Rev. A 34(3), 2499–2500 (1986)
Hoover, W.G.: Canonical dynamics: equilibrium phase-space distributions. Phys. Rev. A 31(3), 1695–1697 (1985)
Nosé, S.: A unified formulation of the constant temperature molecular dynamics method. J. Chem. Phys. 81(1), 511–519 (1984)
Nosé, S.: A molecular-dynamics method for simulations in the canonical ensemble. Mol. Phys. 52 (2), 255–68 (1984)
Tuckerman, M., Berne, B.J., Martyna, G.J.: Reversible multiple time scale molecular dynamics. J. Chem. Phys. 97(3), 1990–2001 (1992)
Darden, T., York, D., Pedersen, L.: Particle Mesh Ewald: An Nlog (N) Method for Ewald sums in large systems. J. Chem. Phys. 98(12), 10089–10092 (1993)
Eastwood, J.W., Hockney, R.W.: Shaping the force law in two-dimensional particle-mesh models. J. Comput. Phys. 16(4), 342–359 (1974)
Verlet, L.: Computer “Experiments” on classical fluids. I. thermodynamical properties of Lennard-Jones molecules. Phys. Rev. 159 (1), 98–103 (1967)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2021 The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.
About this chapter
Cite this chapter
Tang (唐晨宇), C., Wang (王延颋), Y. (2021). Basics of Molecular Modeling and Molecular Simulation. In: Liu, XY. (eds) Frontiers and Progress of Current Soft Matter Research. Soft and Biological Matter. Springer, Singapore. https://doi.org/10.1007/978-981-15-9297-3_5
Download citation
DOI: https://doi.org/10.1007/978-981-15-9297-3_5
Published:
Publisher Name: Springer, Singapore
Print ISBN: 978-981-15-9296-6
Online ISBN: 978-981-15-9297-3
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)