New faster CHARMM molecular dynamics engine

Journal of Computational Chemistry

Volumn 35, Issue 5, 2014, Pages 406-413

  Hynninen, Antti Pekka ^a   Crowley, Michael F ^a  

^a NATIONAL RENEWABLE ENERGY LABORATORY   (United States)

Author keywords

CHARMM; domain decomposition; molecular dynamics; parallel programming

Indexed keywords

CHARMM; CPU CORES; PARALLEL EXECUTIONS; PARALLELIZATIONS; SINGLE CPU;

DOMAIN DECOMPOSITION METHODS; ENGINES; PARALLEL PROGRAMMING;

MOLECULAR DYNAMICS;

ALGORITHM; ARTICLE; CHARMM; COMPUTER PROGRAM; DOMAIN DECOMPOSITION; MOLECULAR DYNAMICS; PARALLEL PROGRAMMING; TIME;

CHARMM; DOMAIN DECOMPOSITION; MOLECULAR DYNAMICS; PARALLEL PROGRAMMING;

ALGORITHMS; MOLECULAR DYNAMICS SIMULATION; SOFTWARE; TIME FACTORS;

EID: 84892868149     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.23501     Document Type: Article

References (13)

1. B. R. Brooks, C. L. Brooks, III, A. D. Mackerell, Jr,., L. Nilsson, R. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. Pastor, C. B. Post, J. Z. Pu, M. Schaefer, B. Tidor, R. M. Venable, H. L. Woodcock, X. Wu, W. Yang, D. M. York, M. Karplus, J. Comput. Chem. 2009, 30, 1545.
2. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, M. Karplus, J. Comput. Chem. 1983, 4, 187.
3. B. Hess, C. Kutzner, D. van der Spoel, E. Lindahl, J. Chem. Theory Comput. 2008, 4, 435.
4. J. C. Phillips, R. Braun, W. Wang, J. Gumbart, E. Tajkhorshid, E. Villa, C. Chipot, R. D. Skeel, L. Kale, K. Schulten, J. Comput. Chem. 2005, 26, 1781.
5. S. J. Plimpton, J. Comput. Phys. 1995, 117, 1.
6. D.A. Case, T. E. Cheatham, III, T. Darden, H. Gohlke, R. Luo, K. M. Merz, Jr,., A. Onufriev, C. Simmerling, B. Wang, R. Woods, J. Comput. Chem. 2005, 26, 1668.
7. K. J. Bowers, R. O. Dror, D. E. Shaw, J. Comput. Phys. 2007, 221, 303.
8. K. J. Bowers, R. O. Dror, D. E. Shaw, J. Chem. Phys. 2006, 124, 184109.
9. T. Darden, D. York, L. Pedersen, J. Chem. Phys. 1993, 98, 10089.
10. D. van der Spoel, E. Lindahl, B. Hess, A. R. van Buuren, E. Apol, P. J. Meulenhoff, D. P. Tieleman, A. L. T. M. Sijbers, K. A. Feenstra, R. van Drunen, H. J. C. Berendsen, Gromacs User Manual version 4.5.4., accessed September 2012, available at: http://www.gromacs.org, 2010.
11. M. Frigo, S. G. Johnson, Proc. IEEE 2005, 93, 216.
12. J.-P. Ryckaert, G. Ciccotti, H. J. C. Berendsen, J. Comput. Phys. 1977, 23, 327.
13. H. H. Loeffler, M. D. Winn, Benchmarks of large biomolecular systems on HPC platforms, accessed September 2012, available at: http://www.stfc.ac.uk/CSE/ randd/cbg/Benchmark/25241.aspx, 2012.