Abstract
In this chapter, we will introduce some practical aspects of molecular dynamics simulations, such as designing the constraints (e.g., SHAKE), periodic boundary conditions, spherical cutoffs, treatment of the long-range interactions (in particular, electrostatic interactions), and identifying the equilibrium states of the simulations.
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References
Allen, M.P., Tildesley, D.J.: Computer Simulation of Liquids. Oxford University Press, New York (1989)
Brooks, B.R., Brooks, C.L., MacKerell, A.D., Nilsson, L., Petrella, R.J., Roux, B., Won, Y., Archontis, G., Bartels, C., Boresch, S., Caflisch, A., Caves, L., Cui, Q., Dinner, A.R., Feig, M., Fischer, S., Gao, J., Hodoscek, M., Im, W., Kuczera, K., Lazaridis, T., Ma, J., Ovchinnikov, V., Paci, E., Pastor, R.W., Post, C.B., Pu, J.Z., Schaefer, M., Tidor, B., Venable, R.M., Woodcock, H.L., Wu, X., Yang, W., York, D.M., Karplus, M.: CHARMM: the biomolecular simulation program. J. Comput. Chem. 30(10), 1545–1614 (2009)
Cheatham III, T.E., Miller, J.L., Fox, T., Darden, T.A., Kollman, P.A.: Molecular dynamics simulations on solvated biomolecular systems: the particle mesh ewald method leads to stable trajectories of DNA, RNA and proteins. J. Am. Chem. Soc. 117, 4193–4194 (1995)
Darden, T., York, D., Perdersen, L.: Particle-mesh Ewald: an \(n\log n\) method for Ewald sums in large systems. J. Chem. Phys. 98, 10089–10092 (1993)
Darden, T.A., Perera, L., Li, L., Pedersen, L.: New tricks for modellers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. Struct. Folding Des. 7, R55–R60 (1999)
Deserno, M., Holm, C.: How to mesh up Ewald sums. I A theoretical and numerical comparison of various particle mesh routines. J. Chem. Phys. 109, 7678–7693 (1998a)
Deserno, M., Holm, C.: How to mesh up Ewald sums. II An accurate error estimate for the particle-particle-particle-mesh algorithm. J. Chem. Phys. 109, 7694–7701 (1998b)
Ding, H., Karasawa, N., Goddard III, W.A.: The reduced cell multipole method for Coulomb interactions in periodic systems with million-atom unit cell. Chem. Phys. Lett. 196, 6–10 (1992)
Ewald, P.: Die Berechnung optischer und elektrostatischer Gitter potenciale. Annalen der Physik 64, 253–287 (1921)
Frenkel, D., Smit, B.: Understanding Molecular Simulation from Algorithms to Applications. Academic, San Diego (2001). ISBN 9780122673511
Fukuda, I., Nakamura, H.: Non-Ewald methods: theory and applications to molecular systems. Biophys. Rev. 4, 161–170 (2012)
Greengard, L., Rokhlin, V.: A fast algorithm for particle simulations. J. Comput. Phys. 73, 325–348 (1987)
Hardy, D.J., Stone, J.E., Vandivort, K.L., Gohara, D., Rodrigues, C., Schulten, K.: Fast molecular electrostatics algorithms on GPUs. In: Wen mei Hwu, W. (ed.) GPU Computing Gems, pp. 43–58. Morgan Kaufmann Publishers, San Francisco (2011)
Hockney, R., Eastwood, J.: Computer simulation using particles. McGraw-Hill, New York (1981)
Hockney, R.W., Eastwood, J.W.: Computer Simulation Using Particles. Adam Hilger, Bristol (1988)
Humphrey, W., Dalke, A., Schulten, K.: VMD − Visual molecular dynamics. J. Mol. Graph. 14, 33–38 (1996)
Leach, A.R.: Molecular Modelling. Principles and Applications, 2nd edn. Pearson Education Limited, Edingburgh Gate/Prentice Hall (2001)
Luty, B.A., David, M.E., Tironi, I.G., van Gunsteren., W.F.: A comparison of particle-particle, particle-mesh and Ewald methods for calculating electrostatic interactions in periodic molecular systems. Mol. Simul. 14, 11–20 (1994)
Luty, B.A., Tironi, I.G., van Gunsteren, W.F.: Lattice-sum methods for calculating electrostatic interactions in molecular simulations. J. Chem. Phys. 103, 3014–3021 (1995)
Phillips, J.C., Stone, J.E., Vandivort, K.L., Armstrong, T.G., Wozniak, J.M., Wilde, M., Schulten, K.: Petascale Tcl with NAMD, VMD, and Swift/T. In: SC’14 Workshop on High Performance Technical Computing in Dynamic Languages. IEEE Press (2014)
Rajagopal, G., Needs, R.: An optimized Ewald method for long-ranged potentials. J. Comput. Phys. 115, 399–405 (1994)
Ryckaert, J.P., Ciccotti, G., Berendsen, H.J.C.: Numerical integration of the Cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J. Comput. Phys. 23, 327–341 (1977)
Schlick, T.: Molecular Modeling and Simulation. An Interdisciplinary Guide, 2nd edn. Springer, New York (2010)
Shimada, J., Kaneko, H., Takada, T.: Efficient calculations of coulombic interactions in biomolecular simulations with periodic boundary conditions. J. Comput. Chem. 14, 867–878 (1993)
Shimada, J., Kaneko, H., Takada, T.: Performance of fast multipole methods for calculating electrostatic interactions in biomacromolecular simulations. J. Comput. Chem. 15, 28–43 (1994)
Stone, J.E., Hardy, D.J., Isralewitz, B., Schulten, K.: GPU algorithms for molecular modelling. In: Bader, D.A., Kurzak, J. (eds.) Scientific Computing with Multicore and Accelerators, pp. 351–371. Chapman & Hall, Boca Raton (2011)
Toukmaji, A.Y., Board, J.A. Jr., Ewald summation techniques in perspective: a survey. Comput. Phys. Commun. 95, 73–92 (1996)
Tuckerman, M.E., Berne, B.J., Martyna, G.J.: Reversible multiple time step scale molecular dynamics. J. Chem. Phys. 97(3), 1990–2001 (1992)
York, D.M., Wlodawer, A., Pedersen, L., Darden, T.A.: Atomic-level accuracy in simulations of large protein crystals. Proc. Natl. Acad. Sci. USA 91, 8715–8718 (1994)
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Kamberaj, H. (2020). Practical Aspects of Molecular Dynamics Simulations. In: Molecular Dynamics Simulations in Statistical Physics: Theory and Applications. Scientific Computation. Springer, Cham. https://doi.org/10.1007/978-3-030-35702-3_10
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DOI: https://doi.org/10.1007/978-3-030-35702-3_10
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