Long time step molecular dynamics using targeted Langevin stabilization

Proceedings of the ACM Symposium on Applied Computing

Volumn , Issue , 2003, Pages 178-182

  Ma, Qun ^a   Izaguirre, Jesus A ^a  

^a University of Notre Dame   (United States)

Author keywords

Long molecular dynamics simulations; Mollified Impulse; Multiple time stepping; Targeted Langevin stabilization; Verlet I r RESPA Impulse

Indexed keywords

COMPUTER SIMULATION; EQUATIONS OF MOTION; HAMILTONIANS; RESONANCE; VECTORS;

MULTIPLE TIME STEPPING;

MOLECULAR DYNAMICS;

EID: 0037661253     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/952562.952570     Document Type: Conference Paper

References (22)

1. E. Barth and T. Schlick. Overcoming stability limitations in biomolecular dynamics. I. Combining force splitting via extrapolation with Langevin dynamics in LN. J. Chem. Phys., 109(5):1617-1632, August 1998.
2. G. Besold, I. Vattulainen, M. Kartunnen, and J. M. Polson. Towards better integrators for dissipative particle dynamics simulations. Physical Review E, 62(6):R7611-R7614, Dec. 2000.
3. J. J. Biesiadecki and R. D. Skeel. Dangers of multiple-time-step methods. J. Comput. Phys., 109(2):318-328, Dec. 1993.
4. T. Bishop, R. D. Skeel, and K. Schulten. Difficulties with multiple timestepping and the fast multipole algorithm in molecular dynamics. J. Comp. Chem., 18(14):1785-1791, Nov. 15, 1997.
5. P. Español and P. B. Warren. Statistical mechanicsof dissipative particle dynamics. Europhys. Lett., 30(4):191-196, May 1 1995.
6. P. Ewald, Die Berechnung optischer und elektrostatischer Gitterpotentiale. Ann. Phys., 64:253-287, 1921.
7. B. García-Archilla, J. M. Sanz-Serna, and R. D. Skeel. Long-time-step methods for oscillatory differential equations. SIAM J. Sci. Comput., 20(3):930-963, Oct. 20, 1998.
8. R. D. Groot and P. B. Warren. Dissipative particle dynamics: Bridging the gap between atomistic and mesoscopic simulation. J. Chem. Phys., 107(11):4423-4435, Sep 15 1997.
9. H. Grubmüller, Dynamiksimulation sehr großer Makromoleküle auf einem Parallelrechner. Master's thesis, Physik-Dept. der Tech. Univ. München, Munich, 1989.
10. H. Grubmüller, H. Heller, A. Windemuth, and K. Schulten. Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions. Molecular Simulation, 6:121-142, 1991.
11. J. A. Izaguirre, D. P. Catarello, J. M. Wozniak, and R. D. Skeel. Langevin stabilization of molecular dynamics. J. Chem. Phys., 114(5):2090-2098, Feb. 1, 2001.
12. J. A. Izaguirre, Q. Ma, T. Matthey, J. Willcock, T. Slabach, B. Moore, and G. Viamontes. Overcoming instabilities in Verlet-I/r-RESPA with the mollified impulse method. In T. Schlick and H. H. Gan, editors, Proceedings of 3rd International Workshop on Methods for Macromolecular Modeling, volume 24 of Lecture Notes in Computational Science and Engineering, pages 146-174. Springer-Verlag, Berlin, New York, 2002.
13. J. A. Izaguirre, S. Reich, and R. D. Skeel. Longer time steps for molecular dynamics. J. Chem. Phys., 110(19):9853-9864, May 15, 1999.
14. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein. Comparison of simple potential functions for simulating liquid water. J. Chem. Phys., 79:926-935, 1983.
15. Q. Ma and J. A. Izaguirre. Targeted mollified impulse method for molecular dynamics. Submitted to J. Chem. Phys., 2002.
16. Q. Ma, J. A. Izaguirre, and R. D. Skeel. Verlet-I/r-RESPA/Impulse is limited by nonlinear instability. Submitted to SIAM Journal on Scientific Computing. Preprint at http://www.nd.edu/̃qma1/pub/MaIS0x.pdf, 2001.
17. T. Matthey and J. A. Izaguirre. ProtoMol: A molecular dynamics framework with incremental parallelization. In Proc. of the Tenth SIAM Conf. on Parallel Processing for Scientific Computing (PP01), Proceedings in Applied Mathematics, Philadelphia, March 2001. Society for Industrial and Applied Mathematics.
18. I. Pagonabarraga, M. H. J. Hagen, and D. Frenkel. Self-consistent dissipative particle dynamics algorithm. Europhys. Lett., 42(4):377-382, May 15 1998.
19. P. Procacci, M. Marchi, and G. J. Martyna. Electrostatic calculations and multiple time scales in molecular dynamics simulation of flexible molecular systems. J. Chem. Phys., 108(21):8799-8803, 1998.
20. J. M. Sanz-Serna and M. P. Calvo. Numerical Hamiltonian Problems. Chapman and Hall, London, 1994.
21. M. Tuckerman, B. J. Berne, and G. J. Martyna. Reversible multiple time scale molecular dynamics. J. Chem. Phys., 97(3):1990-2001, 1992.
22. R. Zhou, E. Harder, H. Xu, and B. J. Berne. Efficient multiple time step method for use with ewald and partical mesh ewald for large biomolecular systems. J. Chem. Phys., 115(5):2348-2358, August 1 2001.