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Journal of Computational Chemistry

Volumn 33, Issue 8, 2012, Pages 868-880

Hybrid particle-field molecular dynamics simulations: Parallelization and benchmarks

(4) Zhao, Ying a,d De Nicola, Antonio a,b Kawakatsu, Toshihiro c Milano, Giuseppe a,b

a UNIVERSITY OF SALERNO (Italy)

b IMAST Scarl Technological District in Polymer and Composite Engineering (Italy)

c TOHOKU UNIVERSITY (Japan)

d DALIAN INSTITUTE OF CHEMICAL PHYSICS (China)

Author keywords

coarse graining; molecular dynamics; parallelization

Indexed keywords

COARSE GRAINING; COMPUTATIONAL COSTS; DENSITY FIELDS; EXPENSIVE PARTS; HYBRID METHOD; HYBRID SCHEME; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR SIMULATIONS; PARALLEL BENCHMARKS; PARALLEL IMPLEMENTATIONS; PARALLELIZATION; PARALLELIZATIONS; PARTICLE DECOMPOSITION; PARTICLE MODEL; PROGRAM PROFILES; SELF CONSISTENT FIELD THEORY; SINGLE PARTICLE;

COMPUTER SIMULATION; MEAN FIELD THEORY; MOLECULAR ORBITALS; SOFTWARE TESTING;

MOLECULAR DYNAMICS;

EID: 84862779907 PISSN: 01928651 EISSN: 1096987X Source Type: Journal
DOI: 10.1002/jcc.22883 Document Type: Article

Times cited : (72)

References (60)

1
- 0003451443
- Oxford University Press: Oxford.
- M. P. Allen, D. J. Tildesley, Computer Simulation of Liquids; Oxford University Press: Oxford, 1989.
- (1989) Computer Simulation of Liquids
- Allen, M.P.¹ Tildesley, D.J.²

2
- 0003705747
- Cambridge University Press: New York.
- D. C. Rapaport, The Art of Molecular Dynamics Simulation; Cambridge University Press: New York, 1996.
- (1996) The Art of Molecular Dynamics Simulation
- Rapaport, D.C.¹

3
- 84862825217
- Academic Press: San Diego, California.
- D. Frenkel, B. Smit, Academic Press: San Diego, California, 2002.
- (2002)
- Frenkel, D.¹ Smit, B.²

4
- 26844470089
- G. Milano, F. Müller-Plathe, J. Phys. Chem. B 2005, 109, 18609.
- (2005) J. Phys. Chem. B , vol.109 , pp. 18609
- Milano, G.¹ Müller-Plathe, F.²

5
- 34249651788
- T. Spyriouni, C. Tzoumanekas, D. Theodorou, F. Muller-Plathe, G. Milano, Macromolecules 2007, 40, 3876.
- (2007) Macromolecules , vol.40 , pp. 3876
- Spyriouni, T.¹ Tzoumanekas, C.² Theodorou, D.³ Muller-Plathe, F.⁴ Milano, G.⁵

6
- 49449113010
- L. Monticelli, S. K. Kandasamy, X. Periole, R. G. Larson, D. P. Tieleman, S.-J. Marrink, J. Chem. Theory. Comput. 2008, 4, 819.
- (2008) J. Chem. Theory. Comput. , vol.4 , pp. 819
- Monticelli, L.¹ Kandasamy, S.K.² Periole, X.³ Larson, R.G.⁴ Tieleman, D.P.⁵ Marrink, S.-J.⁶

7
- 0025048105
- M. Karplus, G. A. Petsko, Nature 1990, 347, 631.
- (1990) Nature , vol.347 , pp. 631
- Karplus, M.¹ Petsko, G.A.²

8
- 0037120092
- F. Müller-Plathe, Chem. Phys. Chem. 2002, 3, 754.
- (2002) Chem. Phys. Chem. , vol.3 , pp. 754
- Müller-Plathe, F.¹

9
- 33746271105
- W. F. van Gunsteren, D. Bakowies, R. Baron, I. Chandrasekhar, M. Christen, X. Daura, P. Gee, D. P. Geerke, A. Glattli, P. H. Hunenberger, M. A. Kastenholz, C. Oostenbrink, M. Schenk, D. Trzesniak, N. F. A. van der Vegt, H. B. Yu, Angew. Chem. Int. Ed. 2006, 45, 4064.
- (2006) Angew. Chem. Int. Ed. , vol.45 , pp. 4064
- Van Gunsteren, W.F.¹ Bakowies, D.² Baron, R.³ Chandrasekhar, I.⁴ Christen, M.⁵ Daura, X.⁶ Gee, P.⁷ Geerke, D.P.⁸ Glattli, A.⁹ Hunenberger, P.H.¹⁰ Kastenholz, M.A.¹¹ Oostenbrink, C.¹² Schenk, M.¹³ Trzesniak, D.¹⁴ Van Der Vegt, N.F.A.¹⁵ Yu, H.B.¹⁶

10
- 41049093757
- M. Praprotnik, L. Delle Site, K. Kremer, Annu. Rev. Phys. Chem. 2008, 59, 545.
- (2008) Annu. Rev. Phys. Chem. , vol.59 , pp. 545
- Praprotnik, M.¹ Delle Site, L.² Kremer, K.³

11
- 12344326258
- Springer-Verlag: Berlin.
- T. Kawakatsu, Statistical Physics of Polymers; Springer-Verlag: Berlin, 2004.
- (2004) Statistical Physics of Polymers
- Kawakatsu, T.¹

12
- 84921903600
- Clarendon Press: Oxford.
- G. H. Fredrickson, The Equilibrium Theory of Inhomogeneous Polymers; Clarendon Press: Oxford, 2006.
- (2006) The Equilibrium Theory of Inhomogeneous Polymers
- Fredrickson, G.H.¹

13
- 3342995995
- M. W. Matsen, M. Schick, Phys. Rev. Lett. 1994, 72, 2660.
- (1994) Phys. Rev. Lett. , vol.72 , pp. 2660
- Matsen, M.W.¹ Schick, M.²

14
- 0000846988
- F. Drolet, G. H. Fredrickson, Phys. Rev. Lett. 1999, 83, 4317.
- (1999) Phys. Rev. Lett. , vol.83 , pp. 4317
- Drolet, F.¹ Fredrickson, G.H.²

15
- 0036140759
- G. H. Fredrickson, V. Ganesan, F. Drolet, Macromolecules 2002, 35, 16.
- (2002) Macromolecules , vol.35 , pp. 16
- Fredrickson, G.H.¹ Ganesan, V.² Drolet, F.³

16
- 31144479456
- Y. Lauw, F. A. M. Leermakers, M. A. Cohen Stuart, J. Phys. Chem. B. 2006, 110, 465.
- (2006) J. Phys. Chem. B. , vol.110 , pp. 465
- Lauw, Y.¹ Leermakers, F.A.M.² Cohen Stuart, M.A.³

17
- 47249163353
- D. Q. Ly, T. Honda, T. Kawakatsu, A. V. Zvelindovsky, Macromolecules 2008, 41, 4501.
- (2008) Macromolecules , vol.41 , pp. 4501
- Ly, D.Q.¹ Honda, T.² Kawakatsu, T.³ Zvelindovsky, A.V.⁴

18
- 33748717996
- E. Dickinson, V. J. Pinfield, D. S. Horne, F. A. M. Leermakers, J. Chem. Soc. Faraday Trans. 1997, 93, 1785.
- (1997) J. Chem. Soc. Faraday Trans. , vol.93 , pp. 1785
- Dickinson, E.¹ Pinfield, V.J.² Horne, D.S.³ Leermakers, F.A.M.⁴

19
- 0032205245
- A. C. Balazs, C. Singh, E. Zhulina, Macromolecules 1998, 31, 8370.
- (1998) Macromolecules , vol.31 , pp. 8370
- Balazs, A.C.¹ Singh, C.² Zhulina, E.³

20
- 0037156198
- J. R. Roan, T. Kawakatsu, J. Chem. Phys. 2002, 116, 7283.
- (2002) J. Chem. Phys. , vol.116 , pp. 7283
- Roan, J.R.¹ Kawakatsu, T.²

21
- 0037156176
- J. R. Roan, T. Kawakatsu, J. Chem. Phys. 2002, 116, 7295.
- (2002) J. Chem. Phys. , vol.116 , pp. 7295
- Roan, J.R.¹ Kawakatsu, T.²

22
- 17644389164
- M. Müller, G. D. Smith, J. Polym. Sci. Part B: Polym. Phys. 2005, 43, 934.
- (2005) J. Polym. Sci. Part B: Polym. Phys. , vol.43 , pp. 934
- Müller, M.¹ Smith, G.D.²

23
- 32644460281
- K. C. Daoulas, M. Müller, M. P. Stoykovich, S. M. Park, Y. J. Papakonstantopoulos, J. J. D. Pablo, P.F. Nealey, H. H. Solak, Phys. Rev. Lett. 2006, 96, 036104.
- (2006) Phys. Rev. Lett. , vol.96 , pp. 036104
- Daoulas, K.C.¹ Müller, M.² Stoykovich, M.P.³ Park, S.M.⁴ Papakonstantopoulos, Y.J.⁵ Pablo, J.J.D.⁶ Nealey, P.F.⁷ Solak, H.H.⁸

24
- 42149145444
- H. Kang, F. A. Detcheverry, A. N. Mangham, M. P. Stoykovich, K. C. Daoulas, R. J. Hamers, M. Müller, J. J. D. Pablo, P. F. Nealey, Phys. Rev. Lett. 2008, 100, 148303.
- (2008) Phys. Rev. Lett. , vol.100 , pp. 148303
- Kang, H.¹ Detcheverry, F.A.² Mangham, A.N.³ Stoykovich, M.P.⁴ Daoulas, K.C.⁵ Hamers, R.J.⁶ Müller, M.⁷ Pablo, J.J.D.⁸ Nealey, P.F.⁹

25
- 47949112884
- F. A. Detcheverry, H. Kang, K. C. Daoulas, M. Müller, P. F. Nealey, J. J. D. Pablo, Macromolecules 2008, 41, 4989.
- (2008) Macromolecules , vol.41 , pp. 4989
- Detcheverry, F.A.¹ Kang, H.² Daoulas, K.C.³ Müller, M.⁴ Nealey, P.F.⁵ Pablo, J.J.D.⁶

26
- 33745656985
- S. W. Sides, B. J. Kim, E. J. Kramer, G. H. Fredrickson, Phys. Rev. Lett. 2006, 96, 250601.
- (2006) Phys. Rev. Lett. , vol.96 , pp. 250601
- Sides, S.W.¹ Kim, B.J.² Kramer, E.J.³ Fredrickson, G.H.⁴

27
- 0346392885
- G. A. Buxton, J. Y. Lee, A. C. Balazs, Macromolecules 2003, 36, 9631.
- (2003) Macromolecules , vol.36 , pp. 9631
- Buxton, G.A.¹ Lee, J.Y.² Balazs, A.C.³

28
- 0037192317
- R. B. Thompson, V. V. Ginzburg, M. W. Matsen, A. C. Balazs, Macromolecules 2002, 35, 1060.
- (2002) Macromolecules , vol.35 , pp. 1060
- Thompson, R.B.¹ Ginzburg, V.V.² Matsen, M.W.³ Balazs, A.C.⁴

29
- 0242384247
- J. Y. Lee, Z. Shou, A. C. Balazs, Phys. Rev. Lett. 2003, 91, 136103.
- (2003) Phys. Rev. Lett. , vol.91 , pp. 136103
- Lee, J.Y.¹ Shou, Z.² Balazs, A.C.³

30
- 67249137750
- G. Milano, T. Kawakatsu, J. Chem. Phys. 2009, 130, 214106.
- (2009) J. Chem. Phys. , vol.130 , pp. 214106
- Milano, G.¹ Kawakatsu, T.²

31
- 79251509579
- G. Milano, T. Kawakatsu, J. Chem. Phys. 2010, 133, 214102.
- (2010) J. Chem. Phys. , vol.133 , pp. 214102
- Milano, G.¹ Kawakatsu, T.²

32
- 0002806690
- L. Dagum, R. Menon, IEEE. Comput. Sci. Eng. 1998, 5, 46.
- (1998) IEEE. Comput. Sci. Eng. , vol.5 , pp. 46
- Dagum, L.¹ Menon, R.²

33
- 0001439335
- M. P. I. Forum, Int. J. Supercomput. App. 1994, 8, 165.
- (1994) Int. J. Supercomput. App. , vol.8 , pp. 165
- Forum, M.P.I.¹

34
- 0029633168
- H. J. C. Berendsen, D. van der Spoel, R. van Drunen, Comput. Phys. Commun. 1995, 91, 43.
- (1995) Comput. Phys. Commun. , vol.91 , pp. 43
- Berendsen, H.J.C.¹ Van Der Spoel, D.² Van Drunen, R.³

35
- 0012652216
- CCLRC, Daresbury Laboratory: Warrington, UK.
- T. R. Forester, W. Smith, DL-POLY User Manual; CCLRC, Daresbury Laboratory: Warrington, UK, 1995.
- (1995) DL-POLY User Manual
- Forester, T.R.¹ Smith, W.²

36
- 0031318387
- J. Stadler, R. Mikulla, H.-R. Trebin, Int. J. Mod. Phys. 1997, 8, 1131.
- (1997) Int. J. Mod. Phys. , vol.8 , pp. 1131
- Stadler, J.¹ Mikulla, R.² Trebin, H.-R.³

37
- 0034206682
- A. P. Lyubartsev, A. Laaksonen, Comput. Phys. Commun. 2000, 128, 565.
- (2000) Comput. Phys. Commun. , vol.128 , pp. 565
- Lyubartsev, A.P.¹ Laaksonen, A.²

38
- 0034650141
- R. Couturier, C. Chipot, Comput. Phys. Commun. 2000, 124, 49.
- (2000) Comput. Phys. Commun. , vol.124 , pp. 49
- Couturier, R.¹ Chipot, C.²

39
- 0034625283
- T. P. Straatsma, M. Philippopoulos, J. A. McCammon, Comput. Phys. Commun. 2000, 128, 377.
- (2000) Comput. Phys. Commun. , vol.128 , pp. 377
- Straatsma, T.P.¹ Philippopoulos, M.² McCammon, J.A.³

40
- 0034625302
- S. Roy, R. Y. Jin, V. Chaudhary, W. L. Hase, Comput. Phys. Commun. 2000, 128, 210.
- (2000) Comput. Phys. Commun. , vol.128 , pp. 210
- Roy, S.¹ Jin, R.Y.² Chaudhary, V.³ Hase, W.L.⁴

41
- 0034857469
- R. Trobec, M. Sterk, D. Janezic, Int. J. Quantum. Chem. 2001, 84, 23.
- (2001) Int. J. Quantum. Chem. , vol.84 , pp. 23
- Trobec, R.¹ Sterk, M.² Janezic, D.³

42
- 0036724126
- S. Goedecker, Comput. Phys. Commun. 2002, 148, 124.
- (2002) Comput. Phys. Commun. , vol.148 , pp. 124
- Goedecker, S.¹

43
- 0037107807
- C. Ozdogan, G. Dereli, T. Cagin, Comput. Phys. Commun. 2002, 148, 188.
- (2002) Comput. Phys. Commun. , vol.148 , pp. 188
- Ozdogan, C.¹ Dereli, G.² Cagin, T.³

44
- 28944432764
- K. B. Tarmyshov, F. Muller-Plathe, J. Chem. Inf. Model 2005, 45, 1943.
- (2005) J. Chem. Inf. Model , vol.45 , pp. 1943
- Tarmyshov, K.B.¹ Muller-Plathe, F.²

45
- 27344436659
- 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.
- (2005) J. Comput. Chem. , vol.26 , pp. 1781
- Phillips, J.C.¹ Braun, R.² Wang, W.³ Gumbart, J.⁴ Tajkhorshid, E.⁵ Villa, E.⁶ Chipot, C.⁷ Skeel, R.D.⁸ Kale, L.⁹ Schulten, K.¹⁰

46
- 77954817911
- B. FrantzDale, S. J. Plimpton, Eng. Comput. 2010, 26, 205.
- (2010) Eng. Comput. , vol.26 , pp. 205
- Frantzdale, B.¹ Plimpton, S.J.²

47
- 64649105762
- M. S. Friedrichs, P. Eastman, V. Vaidyanathan, M. Houston, S. Legrand, A. L. Beberg, D. L. Ensign, C. M. Bruns, V. S. Pande, J. Comput. Chem. 2009, 30, 864.
- (2009) J. Comput. Chem. , vol.30 , pp. 864
- Friedrichs, M.S.¹ Eastman, P.² Vaidyanathan, V.³ Houston, M.⁴ Legrand, S.⁵ Beberg, A.L.⁶ Ensign, D.L.⁷ Bruns, C.M.⁸ Pande, V.S.⁹

48
- 84862813004
- P. Larsson, B. Hess, E. Lindahl, Wiley Interdisciplinary Reviews: Computational Molecular Science 2011, 1, 93.
- (2011) Wiley Interdisciplinary Reviews: Computational Molecular Science , vol.1 , pp. 93
- Larsson, P.¹ Hess, B.² Lindahl, E.³

49
- 84947351879
- D. Finchama, Mol. Simul. 1987, 1, 1.
- (1987) Mol. Simul. , vol.1 , pp. 1
- Finchama, D.¹

50
- 0026120011
- W. Smith, Comput. Phys. Commun. 1991, 62, 229.
- (1991) Comput. Phys. Commun. , vol.62 , pp. 229
- Smith, W.¹

51
- 0007139391
- S. Gupta, Comput. Phys. Commun. 1992, 70, 243.
- (1992) Comput. Phys. Commun. , vol.70 , pp. 243
- Gupta, S.¹

52
- 0002467378
- S. Plimpton, J. Comput. Phys. 1995, 117, 1.
- (1995) J. Comput. Phys. , vol.117 , pp. 1
- Plimpton, S.¹

53
- 0034625278
- G. S. Heffelfinger, Comput. Phys. Commun. 2000, 128, 219.
- (2000) Comput. Phys. Commun. , vol.128 , pp. 219
- Heffelfinger, G.S.¹

54
- 80052807043
- A. De Nicola, Y. Zhao, T. Kawakatsu, D. Roccatano, G. Milano, J. Chem. Theory Comput. 2011, 7, 2947.
- (2011) J. Chem. Theory Comput. , vol.7 , pp. 2947
- De Nicola, A.¹ Zhao, Y.² Kawakatsu, T.³ Roccatano, D.⁴ Milano, G.⁵

55
- 84862832519
- Available at.
- G. Milano, Available at https://www.molnac.unisa.it/occam/, 2007.
- (2007)
- Milano, G.¹

56
- 84862832520
- New York, NY, USA
- S. L. Graham, P. B. Kessler, M. K. Mckusick, ACM SIGPLAN Notices, In Proceedings of the 1982 SIGPLAN Symposium on Compiler Construction, New York, NY, USA, 1982.
- (1982) ACM SIGPLAN Notices, in Proceedings of the 1982 SIGPLAN Symposium on Compiler Construction
- Graham, S.L.¹ Kessler, P.B.² McKusick, M.K.³

57
- 33645998439
- S. S. Shende, A. D. Malony, Int. J. High Perform Comput. 2006, 20, 287.
- (2006) Int. J. High Perform Comput. , vol.20 , pp. 287
- Shende, S.S.¹ Malony, A.D.²

58
- 77950142331
- A. Liwo, S. Oldziej, C. Czaplewski, D. S. Kleinerman, P. Blood, H. A. Scheraga, J. Chem. Theory Comput. 2010, 6, 890.
- (2010) J. Chem. Theory Comput. , vol.6 , pp. 890
- Liwo, A.¹ Oldziej, S.² Czaplewski, C.³ Kleinerman, D.S.⁴ Blood, P.⁵ Scheraga, H.A.⁶

59
- 0040080197
- C. R. Mechoso, J. D. Farrara, J. A. Spahr, IEEE Parallel Distr. Technol. 1994, 2, 57.
- (1994) IEEE Parallel Distr. Technol. , vol.2 , pp. 57
- Mechoso, C.R.¹ Farrara, J.D.² Spahr, J.A.³

60
- 46249092554
- B. Hess, C. Kutzner, D. V. D. Spoel, E. Lindahl, J. Chem. Theory Comput. 2008, 4, 435.
- (2008) J. Chem. Theory Comput. , vol.4 , pp. 435
- Hess, B.¹ Kutzner, C.² Spoel, D.V.D.³ Lindahl, E.⁴

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