Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers

SoftwareX

Volumn 1-2, Issue , 2015, Pages 19-25

  Abraham, Mark James ^a   Murtola, Teemu ^d   Schulz, Roland ^b,c   Páll, Szilárd ^a   Smith, Jeremy C ^b,c   Hess, Berk ^a   Lindah, Erik ^a,d  

^a ROYAL INSTITUTE OF TECHNOLOGY   (Sweden)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF TENNESSEE   (United States)

^d STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

Free energy; Gpu; Molecular dynamics; Simd

Indexed keywords

DOMAIN DECOMPOSITION METHODS; GRAPHICS PROCESSING UNIT; MOLECULAR DYNAMICS; MULTITASKING; OPEN SOURCE SOFTWARE; OPEN SYSTEMS; SUPERCOMPUTERS;

DYNAMICAL SIMULATION; FREE-ENERGY CALCULATIONS; GPU ACCELERATIONS; MOLECULAR SIMULATIONS; MULTI-LEVEL PARALLELISM; PARALLELIZATION ALGORITHMS; SIMD; TRAJECTORY STORAGES;

FREE ENERGY;

EID: 84946416234     PISSN: None     EISSN: 23527110     Source Type: Journal    
DOI: 10.1016/j.softx.2015.06.001     Document Type: Article

References (47)

1. Pronk S, Páll S, Schulz R, Larsson P, Bjelkmar P, Apostolov R, et al. Bioinf 2013;29:845-54.
2. Case DA, Cheatham TE, Darden T, Gohlke H, Luo R, Merz KM, et al. J Comput Chem 2005;26:1668-88.
3. Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, et al. J Comput Chem 2005;26:1781-802.
4. Brooks BR, Bruccoleri RE, Olafson BD, States DJ, Swaminathan S, Karplus M. J Comput Chem 1983;4:187-217.
5. Plimpton S. J Comp Phys 1995;117:1-19.
6. Bowers KJ, Chow E, Xu H, Dror RO, Eastwood MP, Gregersen BA, et al. , Proceedings of the ACM/IEEE conference on supercomputing; 2006. p. 0-7695-2700-0/06.
7. Shirts M, Pande VS. Science 2000;290:1903-4.
8. Tribello GA, Bonomi M, Branduardi D, Camilloni C, Bussi G. Comput Phys Commun 2014;185:604-13.
9. Marrink SJ, Risselada HJ, Yefimov S, Tieleman DP, de Vries AH. J Phys Chem B 2007;111:7812-24.
10. Caleman C, van Maaren PJ, Hong M, Hub JS, Costa LT, van der Spoel D. J Chem Theory Comput 2012;8:61-74.
11. van der Spoel D, van Maaren PJ, Caleman C. Bioinf 2012;28:752-3.
12. Zoete V, Cuendet MA, Grosdidier A, Michielin O. J Comp Chem 2011; 32:2359-68.
13. Malde AK, Zuo L, Breeze M, Stroet M, Poger D, Nair PC, et al. J Chem Theory Comput 2011;7:4026-37.
14. Ryckaert JP, Ciccotti G, Berendsen HJ. J Comput Phys 1977;23:327-41.
15. Hess B, Bekker H, Berendsen HJ, Fraaije JG. J Comput Chem 1997;18: 1463-72.
16. Hess B. J Chem Theory Comput 2008;4:116-22.
17. Berendsen HJC, van Gunsteren WF. In: AJB, et al., editors. Molecular liquids-dynamics and interactions, NATO ASI C 135. Dordrecht (The Netherlands): Reidel; 1984. p. 475-500.
18. Mitsutake A, Sugita Y, Okamoto Y. Biopolymers 2001;60:96-123.
19. Hansmann UH, Okamoto Y. J Comput Chem 1997;18:920-33.
20. Sugita Y, Okamoto Y. Chem Phys Lett 1999;314:141-51.
21. Amadei A, Lisnsen A, Berendsen H. Proteins: Struct, Func, Genet 1993; 17:412-25.
22. Humphrey W, Dalke A, Schulten K. J Mol Graph 1996;14:33-8.
23. Páll S, Abraham MJ, Kutzner C, Hess B, Lindahl E. In: Markidis S, Laure E, editors. Solving software challenges for exascale. Lecture notes in computer science. Springer International Publishing; 2015. p. 3-27.
24. Bekker H, Berendsen HJC, Dijkstra EJ, Achterop S, van Drunen R, van der Spoel D, et al. In: de Groot RA, Nadrchal J, editors. Physics computing, vol. 92. Singapore: World Scientific; 1993. p. 252-6.
25. Berendsen HJ, van der Spoel D, van Drunen R. Comput Phys Commun 1995;91:43-56.
26. Lindahl E, Hess B, van der Spoel D. J Mol Mod 2001;7:306-17.
27. van der Spoel D, Lindahl E, Hess B, Groenhof G, Mark AE, Berendsen HJ. J Comput Chem 2005;26:1701-18.
28. Hess B, Kutzner C, van der Spoel D, Lindahl E. J Chem Theory Comput 2008;4:435-47.
29. Pronk S, Pouya I, Lundborg M, Rotskoff G, Wesén B, Kasson PM, et al. J Chem Theory Comput 2015;11:2600-8.
30. Pan AC, Roux B. J Chem Phys 2008;129:064107.
31. Bowers KJ, Dror RO, Shaw DE. J Phys: Conf Ser 2005;16:300.
32. Bowers KJ, Dror RO, Shaw DE. J Comput Phys 2007;221:303-29.
33. Darden T, York D, Pedersen L. J Chem Phys 1993;98:10089-92.
34. Páll S, Hess B. Comp Phys Comm 2013;184:2641-50.
35. Bekker H, Berendsen HJC, Dijkstra EJ, Achterop S, Drunen RV, Spoel DVD, et al. In: de Groot RA, Nadrchal J, editors. Physics computing, vol. 92. Singapore: World Scientific; 1993. p. 257-61.
36. Wennberg CL, Murtola T, Hess B, Lindahl E. J Chem Theory Comput 2013;9:3527-37.
37. Fritsch S, Junghans C, Kremer K. J Chem Theory Comput 2012;8: 398-403.
38. Lyubartsev AP, Martsinovski AA, Shevkunov SV, Vorontsov-Velyaminov PN. J Chem Phys 1992;96:1776-83.
39. Kutzner C, Czub J, Grubmüller H. J Chem Theory Comput 2011;7: 1381-93.
40. Kutzner C, Grubmüller H, de Groot BL, Zachariae U. Biophys J 2011; 101:809-17.
41. Stone JE, Gullingsrud J, Schulten K. Proceedings of the 2001 symposium on interactive 3D graphics. New York (NY, USA): ACM; 2001. p. 191-4.
42. Salmon JK, Moraes MA, Dror RO, Shaw DE. Proceedings of 2011 international conference for high performance computing, networking, storage and analysis. New York (NY, USA): ACM; 2011. p. 16:1-:12.
43. Bulacu M, Goga N, Zhao W, Rossi G, Monticelli L, Periole X, et al. J Chem Phys 2005;123:3282-892.
44. Lundborg M, Apostolov R, Spångberg D, Gärdenäs A, van der Spoel D, Lindahl E. J Comp Chem 2014;35:260-9.
45. Henrion U, Renhorn J, Börjesson SI, Nelson EM, Schwaiger CS, Bjelkmar P, et al. Proc Natl Acad Sci 2012;109:8552-7.
46. Yoluk O, Brömstrup T, Bertaccini EJ, Trudell JR, Lindahl E. Biophys J 2013;105:640-7.
47. Bussi G, Donadio D, Parrinello M. J Chem Phys 2007;126:014101.