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The Hitchhiker’s guide to molecular dynamics

A lecture companion, mostly for master’s and PhD students interested in using molecular dynamics simulations
  • Philippe A. Bopp
  • Ewa Hawlicka
  • Siegfried Fritzsche
Lecture Text
  • 165 Downloads

Abstract

This lecture aims at advanced (master’s, PhD) students in physics, chemistry, physical chemistry, biochemistry, engineering (and possibly biology) who use, or plan to use, molecular dynamics (MD) computer simulations in the course of their research work. This lecture is, however, neither (or only in a very limited way) a course on the scientific background of this method (quantum mechanics, statistical mechanics, computational methods), nor is it a pragmatics tutorial (‘how-to’ guide) which button to click on some graphical interface or other. We rather aim at pointing out to the aspiring user of any kind of simulation software some of the important choices that must be made as well as some of the problems and pitfalls that he or she may encounter on the way to reliable and meaningful scientific results. This includes a few reminders what not to forget to avoid such mistakes and possibly where to look to correct them if they have, unavoidably, been made.

Keywords

Computational chemistry Molecular simulations Molecular dynamics (MD) Statistical mechanics 

Notes

Acknowledgements

This lecture is the result of many years’ work, making errors and fixing them, together with (present and former) students. We thank in particular Andreas, Christian, Gabriel, Godehard, Guillaume, Holger, Ildiko, Jörn, Kai, Liem, Markus, Michael, Norbert, Patrick, Philipp, Pia, Pooneh, Rungroj(Shaw), Samuel, Siwarut(Jeff), Tanin(Bom), Willi, and several others, and also far too many colleagues to enumerate.

References

  1. 1.
    Web-page. The Hitchhiker’s Guide to the Galaxy. https://en.wikipedia.org/wiki/The_Hitchhiker’s_Guide_to_the_Galaxy. Accessed 5 July 2017
  2. 2.
    Allen MP, Tildesley D (1987) Computer simulations of liquids, Reprint edn. Oxford Science Publications, OxfordGoogle Scholar
  3. 3.
    Frenkel D, Smit B (2002) Understanding molecular simulation, from algorithms to applications. Elsevier, AmsterdamGoogle Scholar
  4. 4.
    McQuarrie DA (1991) Stastical mechanics. Harper & Row, New YorkGoogle Scholar
  5. 5.
    Web-page. Molecular dynamics. https://en.wikipedia.org/wiki/Molecular_dynamics. Accessed 19 July 2017
  6. 6.
    Web-page. Comparison of software for molecular mechanics modeling. https://en.wikipedia.org/wiki/Comparison_of_software_for_molecular_mechanics_modeling. Accessed 5 July 2017
  7. 7.
    Web-page. Born-Oppenheimer approximation. https://en.wikipedia.org/wiki/Born-Oppenheimer approximation. Accessed 20 July 2017
  8. 8.
    Web-page. Thermal de Broglie wavelength. https://en.wikipedia.org/wiki/Thermal_de_Broglie_wavelength. Accessed 6 Jan 2018
  9. 9.
    Web-page. Normal mode. https://en.wikipedia.org/wiki/Normal_mode. Accessed 17 Jan 2018
  10. 10.
    Morawietz T, Marsalek O, Pattenaude SR, Streacker LM, Ben-Amotz D, Markland TE (2017) The interplay of structure and dynamics in the raman spectrum of liquid water over the full frequency and temperature range. arXiv:1711.08563vl, 23 Nov 2017
  11. 11.
    Web-page. European Materials Modelling Council (EMMC) focused workshop Uppsala June 2017. https://drive.google.com/file/d/0B8NBUmVWdMcmTlRmR0dnc2JDUTA/view. Accessed 5 July 2017
  12. 12.
    Hoover WG (1991) Computational statistical mechanics. Elsevier Science, AmsterdamGoogle Scholar
  13. 13.
    Hasse H (2017) The human error, the systematic error and the statistical error. Lecture given at the Focussed Workshop on Modelling Quality & Accuracy, Uppsala June 15–16, 2017Google Scholar
  14. 14.
    Web-page. PACKMOL Initial configurations for Molecular Dynamics Simulations. http://www.ime.unicamp.br/~martinez/packmol/home.shtml. Accessed 15 July 2017
  15. 15.
    Web-page. RSCB PDB, Protein Data Bank. https://www.rcsb.org/pdb/home/home.do. Accessed 20 July 2017
  16. 16.
    Guillot B (2002) A reappraisal of what we have learnt during three decades of computer simulations on water. J Mol Liq 101(1–3):219–260CrossRefGoogle Scholar
  17. 17.
    Hasse H, Lenhard J (2017) Boon and bane: On the role of adjustable parameters in simulation models. In: Lenhard J, Carrier M (eds) Mathematics as a tool. Boston Studies in the Philosophy and History of Science. (reprint requsts to: http://thermo.mv.uni-kl.de/publications/publications/?L=1%2Findex.php%3Fid), 327, Springer 2017
  18. 18.
    Faller R, Schmitz H, Biermann O, Müller-Plathe F (1999) Automatic parameterization of force fields for liquids by simplex optimization. J Comput Chem 20(10):1009–1017CrossRefGoogle Scholar
  19. 19.
    Reith D, Pütz M, Müller-Plathe F (2003) Deriving effective mesoscale potentials from atomistic simulations. J Comput Chem 24(13):1624–1636CrossRefGoogle Scholar
  20. 20.
    Baranyai A, Kiss PT (2010) A transferable classical potential for the water molecule. J Chem Phys 133:144109CrossRefGoogle Scholar
  21. 21.
    Voltaire (François-Marie Arouet). Candide, ou l’Optimisme 1759Google Scholar
  22. 22.
    Marchand G, Soetens J-C, Bopp PA, Jacquemin D (2015) Effect of the cation model on the equilibrium structure of poly-l-glutamate in aqueous sodium chloride solution. J Chem Phys 143:224505CrossRefGoogle Scholar
  23. 23.
    Kanta-Giri A, Spohr E (2017) Cluster formation of NaCl in bulk solutions: Arithmetic vs. geometric combination rules. J Mol Liq 228:63–70CrossRefGoogle Scholar
  24. 24.
    Pethes I (2017) A comparison of classical interatomic potentials applied to highly concentrated aqueous lithium chloride solutions. J Mol Liq 242:845–858CrossRefGoogle Scholar
  25. 25.
    Sutton AP, Chen J (1990) Long-range Finnis-Sinclair potentials. Phil Mag Let 61(1):139–146CrossRefGoogle Scholar
  26. 26.
    Cukier RI (2004) Quantum molecular dynamics simulation of proton transfer in cytochrome c oxidase. Biochim Biophys Acta 1656:189–202CrossRefGoogle Scholar
  27. 27.
    Web-page. Energy Unit Converter. http://www.colby.edu/chemistry/PChem/Hartree.html. Accessed 11 July 2017
  28. 28.
    Web-page. Combining rules. https://en.wikipedia.org/wiki/Combining_rules. Accessed 11 July 2017
  29. 29.
    Reißer S, Poger D, Stroet M, Mark AE (2017) The real cost of speed: the effect of a time-saving multiple-time-stepping algorithm on the accuracy of molecular dynamics simulations. J Chem Theory Comput 13(6):2367–2372CrossRefGoogle Scholar
  30. 30.
    Toxvaerd S (1991) Algorithms for canonical molecular dynamics simulations. Mol Phys 72(1):159–168CrossRefGoogle Scholar
  31. 31.
    Toxvaerd S (1993) Molecular dynamics at constant temperature and pressure. Phys Rev E 47:343–350CrossRefGoogle Scholar
  32. 32.
    Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684–3690CrossRefGoogle Scholar
  33. 33.
    Nosé S (1984) A molecular dynamics method for simulations in the canonical ensemble. Mol Phys 52:255–268CrossRefGoogle Scholar
  34. 34.
    Posch HA, Hoover WG, Vesely FJ (1986) Canonical dynamics of the Nose oscillator: stability, order, and chaos. Phys Rev A 33:4253–4265CrossRefGoogle Scholar
  35. 35.
    Harvey SC, Tan RK, Cheatham E III (1998) The flying ice cube: velocity rescaling in molecular dynamics leads to violation of energy equipartition. J Comp Chem 19:726–740CrossRefGoogle Scholar
  36. 36.
    Grossfield A, Zuckerman DM (2009) Quantifying uncertainty and sampling quality in biomolecular simulations. Annu Rep Comput Chem 5:23–48CrossRefGoogle Scholar
  37. 37.
    Web-page. Molecular dynamics. https://en.wikipedia.org/wiki/Molecular_dynamics Accessed 5 July 2017
  38. 38.
    Web-page. Visual molecular dynamics. http://www.ks.uiuc.edu/Research/vmd/. Accessed 5 July 2017
  39. 39.
    Web-page. List of free and open-source software packages. https://en.wikipedia.org/wiki/List_of_free_and_open-source_software_packages. Accessed 5 July 2017
  40. 40.
    Jacob CR (2016) How open is commercial scientific software? J Phys Chem Lett 7(2):351–353CrossRefGoogle Scholar
  41. 41.
    Web-page. gnuplot home page. https://www.libreoffice.org/. Accessed 5 July 2017
  42. 42.
    Web-page. Xfig User-Manual. http://mcj.sourceforge.net/. Accessed 5 July 2017
  43. 43.
    Web-page. Libre Office, The Document Foundation. http://www.gnuplot.info/. Accessed 10 July 2017
  44. 44.
    Web-page. MOLDEN a pre- and post processing program of molecular and electronic structure. http://www.cmbi.ru.nl/molden/. Accessed 12 July 2017
  45. 45.
    Web-page. Home Page for RasMol and OpenRasMol http://www.openrasmol.org/. Accessed 12 July 2017
  46. 46.
    Yeh I-C, Hummer G (2004) System-size dependence of diffusion coefficients and viscosities from molecular dynamics simulations with periodic boundary conditions. J Phys Chem B 108:15873–15879CrossRefGoogle Scholar
  47. 47.
    Soetens J-C, Bopp PA (2015) Water-methanol mixtures: simulations of excess properties over the entire range of mole fractions. J Phys Chem B 119:8593–8599CrossRefGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  • Philippe A. Bopp
    • 1
  • Ewa Hawlicka
    • 2
  • Siegfried Fritzsche
    • 3
  1. 1.Department of Material Science and Engineering, School of Molecular Science and EngineeringVidyasirimedhi Institute of Science and Technology (VISTEC)RayongThailand
  2. 2.Międzyresortowy Instytut Techniki RadiacyjnePolitechnikaŁódzkaPoland
  3. 3.Fakultät für Physik und Geowissenschaften, Institut für Theoretische PhysikUniversität LeipzigLeipzigGermany

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