Thermalized Drude Oscillators with the LAMMPS Molecular Dynamics Simulator

Journal of Chemical Information and Modeling

Volumn 56, Issue 1, 2016, Pages 260-268

  Dequidt, Alain ^a   Devémy, Julien ^a   Pádua, Agílio A H ^a,b  

^a ICCF   (France)

^b Massachusetts Institute of Technology   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SOFTWARE;

COMPUTATIONAL PERFORMANCE; CUSTOMIZABLE; DRUDE OSCILLATORS; MOLECULAR DYNAMICS SIMULATIONS; REFERENCE SOFTWARE;

MOLECULAR DYNAMICS;

CONFORMATION; INFORMATION RETRIEVAL; MOLECULAR DYNAMICS; PRESSURE; TEMPERATURE;

INFORMATION STORAGE AND RETRIEVAL; MOLECULAR CONFORMATION; MOLECULAR DYNAMICS SIMULATION; PRESSURE; TEMPERATURE;

EID: 84955451107     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00612     Document Type: Article

References (35)

1. Grimme, S.; Antony, J.; Ehrlich, S.; Krieg, H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu J. Chem. Phys. 2010, 132, 154104 10.1063/1.3382344
2. Tkatchenko, A.; Scheffler, M. Accurate Molecular Van Der Waals Interactions from Ground-State Electron Density and Free-Atom Reference Data Phys. Rev. Lett. 2009, 102, 073005 10.1103/PhysRevLett.102.073005
3. Plimpton, S. J. Fast Parallel Algorithms for Short-Range Molecular Dynamics J. Comput. Phys. 1995, 117, 1-19 10.1006/jcph.1995.1039
4. Rick, S. W.; Stuart, S. J. Potentials and algorithms for incorporating polarizability in computer simulations; Reviews in Computational Chemistry 18; John Wiley & Sons Inc.: Hoboken, NJ, 2002; pp 89-146.
5. Onsager, L. Electric Moments of Molecules in Liquids J. Am. Chem. Soc. 1936, 58, 1486-1493 10.1021/ja01299a050
6. Kirkwood, J. G. The Dielectric Polarization of Polar Liquids J. Chem. Phys. 1939, 7, 911 10.1063/1.1750343
7. Stillinger, F. H.; David, C. W. Polarization Model for Water and its Ionic Dissociation Products J. Chem. Phys. 1978, 69, 1473-1484 10.1063/1.436773
8. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The Missing Term in Effective Pair Potentials J. Phys. Chem. 1987, 91, 6269-6271 10.1021/j100308a038
9. Sprik, M.; Klein, M. L. A Polarizable Model for Water Using Distributed Charge Sites J. Chem. Phys. 1988, 89, 7556 10.1063/1.455722
10. Nalewajski, R. F. A. Study of Electronegativity Equalization J. Phys. Chem. 1985, 89, 2831-2837 10.1021/j100259a025
11. Rappe, A. K.; Goddard, W. A. Charge Equilibration for Molecular Dynamics Simulations J. Phys. Chem. 1991, 95, 3358-3363 10.1021/j100161a070
12. Rick, S. W.; Stuart, S. J.; Berne, B. J. Dynamical Fluctuating Charge Force Fields: Application to Liquid Water J. Chem. Phys. 1994, 101, 6141-6156 10.1063/1.468398
13. Smirnov, K. S.; Graaf, B. v. d. Consistent Implementation of the Electronegativity Equalization Method in Molecular Mechanics and Molecular Dynamics J. Chem. Soc., Faraday Trans. 1996, 92, 2469-2474 10.1039/ft9969202469
14. Drude, P. The theory of optics; Lehrbuch der Optik; Longmans, Green, and Co.: London/New York, 1902.
15. van Maaren, P. J.; van der Spoel, D. Molecular Dynamics Simulations of Water with Novel Shell-Model Potentials J. Phys. Chem. B 2001, 105, 2618-2626 10.1021/jp003843l
16. Lamoureux, G.; Roux, B. Modeling Induced Polarization with Classical Drude Oscillators: Theory and Molecular Dynamics Simulation Algorithm J. Chem. Phys. 2003, 119, 3025-3039 10.1063/1.1589749
17. Lopes, P. E. M.; Roux, B.; Mackerell, A. D. Molecular Modeling and Dynamics Studies with Explicit Inclusion of Electronic Polarizability: Theory and Applications Theor. Chem. Acc. 2009, 124, 11-28 10.1007/s00214-009-0617-x
18. Huang, J.; Lopes, P. E. M.; Roux, B.; MacKerell, A. D., Jr. Recent Advances in Polarizable Force Fields for Macromolecules: Microsecond Simulations of Proteins Using the Classical Drude Oscillator Model J. Phys. Chem. Lett. 2014, 5, 3144-3150 10.1021/jz501315h
19. Bauer, B. A.; Patel, S. Recent Applications and Developments of Charge Equilibration Force Fields for Modeling Dynamical Charges in Classical Molecular Dynamics Simulations Theor. Chem. Acc. 2012, 131, 1153-1155 10.1007/s00214-012-1153-7
20. Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. An Overview of the Amber Biomolecular Simulation Package WIRES: Comput. Mol. Sci. 2013, 3, 198-210 10.1002/wcms.1121
21. Baker, C. M.; Best, R. B. Matching of Additive and Polarizable Force Fields for Multiscale Condensed Phase Simulations J. Chem. Theory Comput. 2013, 9, 2826-2837 10.1021/ct400116g
22. Mitchell, P. J.; Fincham, D. Shell Model Simulations by Adiabatic Dynamics J. Phys.: Condens. Matter 1993, 5, 1031-1038 10.1088/0953-8984/5/8/006
23. Todorov, I. T.; Smith, W.; Trachenko, K.; Dove, M. T. DL-POLY-3: New Dimensions in Molecular Dynamics Simulations via Massive Parallelism J. Mater. Chem. 2006, 16, 1911 10.1039/b517931a
24. 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. 2009, 30, 1545-1614 10.1002/jcc.21287
25. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
26. Harder, E.; Anisimov, V. M.; Vorobyov, I. V.; Lopes, P. E. M.; Noskov, S. Y.; MacKerell, A. D.; Roux, B. Atomic Level Anisotropy in the Electrostatic Modeling of Lone Pairs for a Polarizable Force Field Based on the Classical Drude Oscillator J. Chem. Theory Comput. 2006, 2, 1587-1597 10.1021/ct600180x
27. Thole, B. T. Molecular Polarizabilities Calculated with a Modified Dipole Interaction Chem. Phys. 1981, 59, 341-350 10.1016/0301-0104(81)85176-2
28. Noskov, S. Y.; Lamoureux, G.; Roux, B. Molecular Dynamics Study of Hydration in Ethanol-Water Mixtures Using a Polarizable Force Field J. Phys. Chem. B 2005, 109, 6705-6713 10.1021/jp045438q
29. Jiang, W.; Hardy, D. J.; Phillips, J. C.; MacKerell, A. D.; Schulten, K.; Roux, B. High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD J. Phys. Chem. Lett. 2011, 2, 87-92 10.1021/jz101461d
30. Kohlmeyer, A. TopoTools, 2014; https://sites.google.com/site/akohlmey/software/topotools.
31. Jewett, A.; Lambert, J. Moltemplate, 2014; http://www.moltemplate.org/.
32. Pádua, A. A. H. fftool: a tool to build force field input files for molecular dynamics, 2015; https://github.com/agiliopadua/fftool.
33. Schröder, C.; Steinhauser, O. Simulating Polarizable Molecular Ionic Liquids with Drude Oscillators J. Chem. Phys. 2010, 133, 154511 10.1063/1.3493689
34. Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D. A Polarizable Model of Water for Molecular Dynamics Simulations of Biomolecules Chem. Phys. Lett. 2006, 418, 245-249 10.1016/j.cplett.2005.10.135
35. Yu, H.; van Gunsteren, W. F. Charge-on-Spring Polarizable Water Models Revisited: From Water Clusters to Liquid Water to Ice J. Chem. Phys. 2004, 121, 9549 10.1063/1.1805516