MOIL-opt: Energy-conserving molecular dynamics on a GPU/CPU system

Journal of Chemical Theory and Computation

Volumn 7, Issue 10, 2011, Pages 3072-3082

  Ruymgaart, A Peter ^a   Cardenas, Alfredo E ^a   Elber, Ron ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 80053970088     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct200360f     Document Type: Article

References (32)

1. Olender, R.; Elber, R. Calculation of classical trajectories with a very large time step: Formalism and numerical examples J. Chem. Phys. 1996, 105 (20) 9299-9315 (Pubitemid 126747963)
2. Dellago, C.; Bolhuis, P. G.; Geissler, P. L. Transition path sampling. In Adv. Chem. Phys.; John Wiley & Sons Inc: New York, 2002; Vol. 123, pp 1-78.
3. Faradjian, A. K.; Elber, R. Computing time scales from reaction coordinates by milestoning J. Chem. Phys. 2004, 120 (23) 10880-10889
4. Majek, P.; Elber, R. Milestoning without a Reaction Coordinate J. Chem. Theory Comput. 2010, 6 (6) 1805-1817
5. Moroni, D.; Bolhuis, P. G.; van Erp, T. S. Rate constants for diffusive processes by partial path sampling J. Chem. Phys. 2004, 120 (9) 4055-4065
6. van Erp, T. S.; Moroni, D.; Bolhuis, P. G. A novel path sampling method for the calculation of rate constants J. Chem. Phys. 2003, 118 (17) 7762-7774
7. Allen, R. J.; Frenkel, D.; ten Wolde, P. R. Forward flux sampling-type schemes for simulating rare events: Efficiency analysis J. Chem. Phys. 2006, 124 (19) 17
8. Elber, R.; West, A. Atomically detailed simulation of the recovery stroke in myosin by Milestoning Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 5001-5005
9. Darden, T.; York, D.; Pedersen, L. Particle mesh ewald-an n.log(n) method for ewald sums in large systems J. Chem. Phys. 1993, 98 (12) 10089-10092
10. Tuckerman, M.; Berne, B. J.; Martyna, G. J. Reversible multiple time scale molecular-dynamics J. Chem. Phys. 1992, 97 (3) 1990-2001
11. Shaw, D. E.; Maragakis, P.; Lindorff-Larsen, K.; Piana, S.; Dror, R. O.; Eastwood, M. P.; Bank, J. A.; Jumper, J. M.; Salmon, J. K.; Shan, Y. B.; Wriggers, W. Atomic-Level Characterization of the Structural Dynamics of Proteins Science 2010, 330 (6002) 341-346
12. Stone, J. E.; Phillips, J. C.; Freddolino, P. L.; Hardy, D. J.; Trabuco, L. G.; Schulten, K. Accelerating molecular modeling applications with graphics processors J. Comput. Chem. 2007, 28 (16) 2618-2640 (Pubitemid 350074136)
13. Harvey, M. J.; Giupponi, G.; De Fabritiis, G. ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale J. Chem. Theory Comput. 2009, 5 (6) 1632-1639
14. Ravikant, D. V. S.; Elber, R. PIE-efficient filters and coarse grained potentials for unbound protein-protein docking Proteins: Struct., Funct., Bioinf. 2010, 78 (2) 400-419
15. Anderson, J. A.; Lorenz, C. D.; Travesset, A. General purpose molecular dynamics simulations fully implemented on graphics processing units J. Comput. Phys. 2008, 227 (10) 5342-5359
16. Elber, R.; Roitberg, A.; Simmerling, C.; Goldstein, R.; Li, H. Y.; Verkhivker, G.; Keasar, C.; Zhang, J.; Ulitsky, A. Moil a program for simulations of macrmolecules Comput. Phys. Commun. 1995, 91 (1-3) 159-189
17. Elber, R.; Ghosh, A.; Cardenas, A. Long time dynamics of complex systems Acc. Chem. Res. 2002, 35 (6) 396-403
18. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical integration of cartesian equations of m otion of a system with constraints-molecular dynamics of N-alkanes J. Comput. Phys. 1977, 23 (3) 327-341
19. Weinbach, Y.; Elber, R. Revisiting and parallelizing SHAKE J. Comput. Phys. 2005, 209 (1) 193-206 (Pubitemid 40792364)
20. van Meel, J. A.; Arnold, A.; Frenkel, D.; Zwart, S. F. P.; Belleman, R. G. Harvesting graphics power for MD simulations Mol. Simul. 2008, 34 (3) 259-266
21. Harvey, M. J.; De Fabritiis, G. An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware J. Chem. Theory Comput. 2009, 5 (9) 2371-2377
22. Morrone, J. A.; Zhou, R. H.; Berne, B. J. Molecular Dynamics with Multiple Time Scales: How to Avoid Pitfalls J. Chem. Theory Comput. 2010, 6 (6) 1798-1804
23. Schnieders, M. J.; Fenn, T. D.; Pande, V. S. Polarizable Atomic Multipole X-Ray Refinement: Particle Mesh Ewald Electrostatics for Macromolecular Crystals J. Chem. Theory Comput. 2011, 7 (4) 1141-1156
24. Yip, V.; Elber, R. Calculation of a list of neighbors in molecular-dynamics simulations J. Comput. Chem. 1989, 10 (7) 921-927
25. Eastman, P.; Pande, V. S. Efficient Nonbonded Interactions for Molecular Dynamics on a Graphics Processing Unit J. Comput. Chem. 2010, 31 (6) 1268-1272
26. Kaminski, G.; Friesner, R.; Tirado-Rives, J.; Jorgensen, W. L. Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides J. Phys. Chem. B 2001, 105 (28) 6474-6487 (Pubitemid 35339015)
27. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of simple potential functions for simulating liquid water J. Chem. Phys. 1983, 79 (2) 926-935
28. Berendsen, H. J. C.; Grigera, J. R.; Straatsma, T. P. The missing term in effective pair potentials J. Phys. Chem. 1987, 91 (24) 6269-6271
29. Jorgensen, W. L.; Tiradorives, J. The OPLS potential functions for proteins-energy minimizations for crystals of cyclic-peptides and crambin J. Am. Chem. Soc. 1988, 110 (6) 1657-1666
30. Berger, O.; Edholm, O.; Jahnig, F. Molecular dynamics simulations of a fluid bilayer of dipalmitoylphosphatidylcholine at full hydration, constant pressure, and constant temperature Biophys. J. 1997, 72 (5) 2002-2013 (Pubitemid 27184429)
31. Gallardo, I. F.; Webb, L. J. Tethering Hydrophobic Peptides to Functionalized Self-Assembled Mono layers on Gold through Two Chemical Linkers Using the Huisgen Cycloaddition Langmuir 2010, 26 (24) 18959-18966
32. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation J. Chem. Theory Comput. 2008, 4 (3) 435-447