High-performance scalable molecular dynamics simulations of a polarizable force field based on classical drude oscillators in NAMD

Journal of Physical Chemistry Letters

Volumn 2, Issue 2, 2011, Pages 87-92

  Jiang, Wei ^a   Hardy, David J ^b   Phillips, James C ^b   MacKerell, Alexander D ^c   Schulten, Klaus ^b,d   Roux, Benoît ^a,e  

^a ARGONNE NATIONAL LABORATORY   (United States)

^b UNIVERSITY OF ILLINOIS AT URBANA CHAMPAIGN   (United States)

^c UNIVERSITY OF MARYLAND SCHOOL OF PHARMACY   (United States)

^d University of Illinois at Urbana Champaign   (United States)

^e UNIVERSITY OF CHICAGO   (United States)

Author keywords

General Theory; Molecular Structure; Quantum Chemistry

Indexed keywords

AQUEOUS SALT SOLUTION; ATOMISTIC MOLECULAR DYNAMICS; CLASSICAL DYNAMICS; COMPUTATIONAL DEMANDS; COMPUTATIONALLY EFFICIENT; CRITICAL CHALLENGES; DISTRIBUTED SUPERCOMPUTING; DRUDE OSCILLATORS; EXTENDED LAGRANGIAN; GENERAL THEORY; INDUCED POLARIZATION; LANGEVIN; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; POLARIZABLE FORCE FIELD; SELF-CONSISTENT FIELD;

CRACK PROPAGATION; MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; OSCILLATORS (ELECTRONIC); QUANTUM CHEMISTRY; QUANTUM THEORY; SODIUM CHLORIDE;

COMPUTER SIMULATION;

EID: 78751688849     PISSN: None     EISSN: 19487185     Source Type: Journal    
DOI: 10.1021/jz101461d     Document Type: Article

References (37)

1. Cornell, W.; Cieplak, P.; Bayly, C.; Gould, I., Jr. ; K., M.; Ferguson, D.; Spellmeyer, D.; Fox, T.; Caldwell, J.; Kollman, P. A Second Generation Force Field for the Simulation of Proteins and Nucleic Acids J. Am. Chem. Soc. 1995, 117, 5179-5197
2. MacKerell, A. D., Jr. All-Hydrogen Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins Using the CHARMM22 Force Field J. Phys. Chem. B 1998, 102, 3586-3616
3. Hermans, J.; Berendsen, H.; van Gunsteren, W.; Postma, J. A Consistent Empirical Potential for Water-Protein Interactions Biopolymers 1984, 23, 1513-1518
4. Jorgensen, W. L.; Tirado-Rives, J. The OPLS Potential Functions for Proteins. Energy Minimization for Crystal of Cyclic Peptides and Crambin J. Am. Chem. Soc. 1988, 110, 1657-1666
5. Caldwell, J. W.; Kollman, P. A. Structure and Properties of Neat Liquids Using Nonadditive Molecular Dynamics: Water, Methanol, and N -Methylacetamide J. Phys. Chem. 1995, 99, 6208-6219
6. Cieplak, P.; Caldwell, J.; Kollman, P. Molecular Mechanical Models for Organic and Biological Systems Going Beyond the Atom Centered Two Body Additive Approximation: Aqueous Solution Free Energies of Methanol and N -Methyl Acetamide, Nucleic Acid Base, and Amide Hydrogen Bonding and Chloroform/Water Partition Coefficients of the Nucleic Acid Bases J. Comput. Chem. 2001, 22, 1048-1057
7. Kaminski, G.; Friesner, R. A.; Zhou, R. A Computationally Inexpensive Modification of the Point Dipole Electrostatic Polarization Model for Molecular Simulations J. Comput. Chem. 2003, 24, 267-276
8. Rick, S. W.; Stuart, S. J.; Bader, J. S.; Berne, B. J. Fluctuating Charge Force Fields for Aqueous Solutions J. Mol. Liq. 1995, 66, 31-40
9. Rick, S. W.; Berne, B. J. Dynamical Fluctuating Charge Force Fields: The Aqueous Solvation of Amides J. Am. Chem. Soc. 1996, 118, 672-679
10. Rick, S. W.; Stuart, S. J.; Berne, B. J. Dynamical Fluctuating Charge Force Field: Application to Liquid Water J. Chem. Phys. 1994, 101, 6141-6156
11. Stern, H. A.; Rittner, F.; Berne, B. J.; Friesner, R. A. Combined Fluctuating Charge and Polarizable Dipole Models: Application to a Five-Site Water Potential Function J. Chem. Phys. 2001, 115, 2237-2251
12. Rick, S. W. Simulations of Ice and Liquid Water over a Range of Temperatures Using the Fluctuating Charge Model J. Chem. Phys. 2001, 114, 2276-2283
13. Lamoureux, G.; Roux, B. Modeling Induced Polarization with Classical Drude Oscillators: Theory and Molecular Dynamics Simulation Algorithm J. Chem. Phys. 2003, 119, 3025-3039
14. Lamoureux, G.; MacKerell, A. D., Jr. ; Roux, B. A Simple Polarizable Model of Water Based on Classical Drude Oscillators J. Chem. Phys. 2003, 119, 5185-5197
15. Anisimov, V. M.; Lamoureux, G.; Vorobyov, I. V.; Huang, N.; Roux, B.; MacKerell, A. D., Jr. Determination of Electrostatic Parameters for a Polarizable Force Field Based on the Classical Drude Oscillator J. Chem. Theory Comput. 2005, 1, 153-168
16. Vorobyov, I. V.; Anisimov, V. M.; MacKerell, A. D., Jr. Polarizable Empirical Force Field for Alkanes Based on the Classical Drude Oscillator Model J. Phys. Chem. B 2005, 109, 18988-18999
17. Lamoureux, G.; Harder, E.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D., Jr. A Polarizable Model of Water for Molecular Dynamics Simulations of Biomolecules Chem. Phys. Lett. 2006, 418, 245-249
18. Harder, E.; Anisimov, V. M.; Vorobyov, I. V.; Lopes, P. E. M.; Noskov, S. Y.; MacKerell, A. D., Jr. ; 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
19. Anisimov, V. M.; Vorobyov, I. V.; Roux, B.; MacKerell, A. D., Jr. Polarizable Empirical Force Field for the Primary and Secondary Alcohol Series Based on the Classical Drude Model J. Chem. Theory Comput. 2007, 3, 1927-1946
20. Lopes, P. E. M.; Lamoureux, G.; Roux, B.; MacKerell, A. D., Jr. Polarizable Empirical Force Field for Aromatic Compounds Based on the Classical Drude Oscillator J. Phys. Chemw. B 2007, 111, 2873-2885
21. Vorobyov, I.; Anisimov, V. M.; Greene, S.; Venable, R. M.; Moser, A.; Pastor, R. W.; MacKerell, A. D., Jr. Additive and Classical Drude Polarizable Force Fields for Linear and Cyclic Ethers J. Chem. Theory Comput. 2007, 3, 1120-1133
22. + Comparing Ab Initio, Polarizable, and Fixed-Charge Models J. Chem. Theory Comput. 2007, 3, 2068-2082
23. Harder, E.; Anisimov, V. M.; Whitfield, T. W.; MacKerell, A. D., Jr. ; Roux, B. Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field J. Phys. Chem. B 2008, 112, 3509-3521
24. Lopes, P. E.; Roux, B.; MacKerell, A. D., Jr. Molecular Modeling and Dynamics Studies with Explicit Inclusion of Electronic Polarizability. Theory and Applications Theor. Chem. Acc. 2009, 124, 11-28
25. Brooks, B. R. CHARMM: The Biomolecular Simulation Program J. Comput. Chem. 2009, 30, 1545-1614
26. Phillips, J.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.; Kale, L.; Schulten, K. Scalable Molecular Dynamics with NAMD J. Comput. Chem. 2005, 26, 1781
27. Lowe, C. An Alternative Approach to Dissipative Particle Dynamics Europhys. Lett. 1999, 47, 145-151
28. Koopman, E. A.; Lowe, C. P. Advantages of a Lowe-Andersen Thermostat in Molecular Dynamics Simulations J. Chem. Phys. 2006, 124, 204103
29. Bruenger, A.; Brooks, C. B.; Karplus, M. Stochastic Boundary Conditions for Molecular Dynamics Simulations of ST2 Water Chem. Phys. Lett. 1984, 105, 495-500
30. Verlet, L. Computer Experiments on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules Phys. Rev. 1967, 159, 98-103
31. Verlet, L. Computer Experiments on Classical Fluids. II. Equilibrium Correlation Functions Phys. Rev. 1968, 165, 201-214
32. Miyamoto, S.; Kollman, P. SETTLE: An Analytical Version of the SHAKE and RATTLE Algorithm for Rigid Water Models J. Comput. Chem. 1992, 13, 952-962
33. Goebel, A.; Lunkenheimer, K. Interfacial Tension of the Water/ N -Alkane Interface Langmuir 1997, 13, 369-372
34. Ponder, J.; Wu, C.; Ren, P.; Pande, V.; Chodera, J.; Schnieders, M.; Haque, I.; Mobley, D.; Lambrecht, D.; DiStasio, R., Jr. Current Status of the AMOEBA Polarizable Force Field J. Phys. Chem. B 2010, 114, 2549-2564
35. Yu, H.; Whitfield, T.; Harder, E.; Lamoureux, G.; Vorobyov, I.; Anisimov, V.; MacKerell, A. D., Jr. ; Roux, B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field J. Chem. Theory Comput. 2010, 6, 774-786
36. Lide, D. R., Ed. CRC Handbook of Chemistry and Physics, 87 th ed.; Taylor and Francis: Boca Raton, FL, 2007.
37. Robinson, R.; Stokes, R. Electrolyte Solutions; Dover Publications: Mineola, NY, 2002.