Scalable evaluation of polarization energy and associated forces in polarizable molecular dynamics: I. Toward massively parallel direct space computations

Journal of Chemical Theory and Computation

Volumn 10, Issue 4, 2014, Pages 1638-1651

  Lipparini, Filippo ^a,b,c   Lagardère, Louis ^c   Stamm, Benjamin ^a,d   Cancès, Eric ^e   Schnieders, Michael ^f   Ren, Pengyu ^g   Maday, Yvon ^a,h,i   Piquemal, Jean Philip ^a,d  

^a UNIVERSITÉ PIERRE ET MARIE CURIE   (France)

^b SORBONNE UNIVERSITÉ   (France)

^c Université Pierre et Marie Curie Muséum national d'Histoire naturelle   (France)

^d CNRS   (France)

^e UNIVERSITÉ PARIS EST   (France)

^f UNIVERSITY OF IOWA   (United States)

^g The University of Texas at Austin   (United States)

^h INSTITUT UNIVERSITAIRE DE FRANCE   (France)

ⁱ BROWN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84898435016     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct401096t     Document Type: Article

References (49)

1. Jorgensen, W. L. J. Chem. Theory Comput. 2007, 3, 1877-1877 and references therein
2. Piquemal, J.-P.; Jordan, K. D. Theor. Chem. Acc. 2012, 131, 1-2
3. Gresh, N.; Cisneros, G. A.; Darden, T. A.; Piquemal, J.-P. J. Chem. Theory Comput. 2007, 3, 1960-1986
4. Warshel, A.; Kato, M.; Pisliakov, A. V. J. Chem. Theory Comput. 2007, 3, 2034-2045
5. Rick, S. W.; Stuart, S. J.; Berne, B. J. J. Chem. Phys. 1994, 101, 6141-6156
6. Rick, S. W.; Stuart, S. J.; Berne, B. J. J. Chem. Phys. 1994, 101, 6141-6156
7. Verstraelen, T.; Speybroeck, V. V.; Waroquier, M. J. Chem. Phys. 2009, 131, 044127
8. Lipparini, F.; Barone, V. J. Chem. Theory Comput. 2011, 7, 3711-3724
9. Piquemal, J.-P.; Chelli, R.; Procacci, P.; Gresh, N. J. Phys. Chem. A 2007, 111, 8170-8176
10. Lamoureux, G.; Roux, B. J. Chem. Phys. 2003, 119, 3025-3039
11. Boulanger, E.; Thiel, W. J. Chem. Theory Comput. 2012, 8, 4527-4538
12. Gordon, M. S.; Smith, Q. A.; Xu, P.; Slipchenko, L. V. Annu. Rev. Phys. Chem. 2013, 64, 553-578
13. Ponder, J. W.; Wu, C.; Ren, P.; Pande, V. S.; Chodera, J. D.; Schnieders, M. J.; Haque, I.; Mobley, D. L.; Lambrecht, D. S.; DiStasio, R. A.; Head-Gordon, M.; Clark, G. N. I.; Johnson, M. E.; Head-Gordon, T. J. Phys. Chem. B 2010, 114, 2549-2564
14. Ren, P.; Ponder, J. W. J. Phys. Chem. B 2003, 107, 5933-5947
15. Applequist, J.; Carl, J. R.; Fung, K.-K. J. Am. Chem. Soc. 1972, 94, 2952-2960
16. Thole, B. Chem. Phys. 1981, 59, 341-350
17. Sala, J.; Guàrdia, E.; Masia, M. J. Chem. Phys. 2010, 133, 234101
18. Wang, W.; Skeel, R. D. J. Chem. Phys. 2005, 123, 164107
19. Sagui, C.; Pedersen, L. G.; Darden, T. A. J. Chem. Phys. 2004, 120, 73-87
20. Lipparini, F.; Cappelli, C.; Barone, V. J. Chem. Theory Comput. 2012, 8, 153-4165
21. Lipparini, F.; Cappelli, C.; Scalmani, G.; De Mitri, N.; Barone, V. J. Chem. Theory Comput. 2012, 8, 4270-4278
22. Lipparini, F.; Cappelli, C.; Barone, V. J. Chem. Phys. 2013, 138, 234108
23. Curutchet, C.; Muñoz-Losa, A.; Monti, S.; Kongsted, J.; Scholes, G. D.; Mennucci, B. J. Chem. Theory Comput. 2009, 5, 1838-1848
24. Caprasecca, S.; Curutchet, C.; Mennucci, B. J. Chem. Theory Comput. 2012, 8, 4462-4473
25. Cisneros, G. A.; Piquemal, J.-P.; Darden, T. A. J. Phys. Chem. B 2006, 110, 13682-13684
26. Ponder, J. W. TINKER Molecular Modeling, Package V 6.2. http://dasher.wustl.edu/tinker/ (accessed July 14, 2013).
27. Schnieders, M. J.; Fenn, T. D.; Pande, V. S. J. Chem. Theory Comput. 2011, 7, 1141-1156
28. Force Field X. http://ffx.eng.uiowa.edu/ (accessed November 14, 2013).
29. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577-8593
30. Cisneros, G. A.; Piquemal, J.-P.; Darden, T. A. J. Chem. Phys. 2006, 125, 184101
31. Tomasi, J.; Mennucci, B.; Cammi, R. Chem. Rev. 2005, 105, 2999-3093
32. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161-2200
33. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129
34. Brancato, G.; Rega, N.; Barone, V. J. Chem. Phys. 2006, 124, 214505
35. Rega, N.; Brancato, G.; Barone, V. Chem. Phys. Lett. 2006, 422, 367-371
36. Klamt, A.; Schuurmann, G. J. Chem. Soc., Perkin Trans. 2 1993, 799-805
37. Cancès, E.; Maday, Y.; Stamm, B. J. Chem. Phys. 2013, 139, 054111
38. Lipparini, F.; Stamm, B.; Cancès, E.; Maday, Y.; Mennucci, B. J. Chem. Theory Comput. 2013, 9, 3637-3648
39. Lipparini, F.; Scalmani, G.; Mennucci, B.; Cancès, E.; Caricato, M.; Frisch, M. J. J. Chem. Phys. 2010, 133, 014106
40. Greengard, L.; Rokhlin, V. J. Comput. Phys. 1987, 73, 325-348
41. Cheng, H.; Greengard, L.; Rokhlin, V. J. Comput. Phys. 1999, 155, 468-498
42. Rohwedder, T.; Schneider, R. J. Math. Chem. 2011, 49, 1889-1914
43. Pulay, P. Chem. Phys. Lett. 1980, 73, 393-398
44. Pulay, P. J. Comput. Chem. 1982, 3, 556-560
45. Shi, Y.; Xia, Z.; Zhang, J.; Best, R.; Wu, C.; Ponder, J. W.; Ren, P. J. Chem. Theory Comput. 2013, 9, 4046-4063
46. Verlet, L. Phys. Rev. 1967, 159, 98-103
47. Swope, W. C.; Andersen, H. C.; Berens, P. H.; Wilson, K. R. J. Chem. Phys. 1982, 76, 637-649
48. Kolafa, J. J. Comput. Chem. 2004, 25, 335-342
49. Piquemal, J.-P.; Cisneros, G. A.; Reinhardt, P.; Gresh, N.; Darden, T. A. J. Chem. Phys. 2006, 124, 104101