[1] |
Brooks B R, Brooks C L, Mackerell A D, et al. 2009 J. Comput. Chem. 30 1545
|
[2] |
Case D A, Cheatham T E, Darden T, Gohlke H, Luo R, Merz K M, Onufriev A, Simmerling C, Wang B and Woods R J 2005 J. Comput. Chem. 26 1668
|
[3] |
Christen M, Hnenberger P H, Bakowies D, et al. 2005 J. Comput. Chem. 26 1719
|
[4] |
Pronk S, Pll S, Schulz R, et al. 2013 Bioinformatics 29 845
|
[5] |
Plimpton S 1995 J. Comput. Phys. 117 1
|
[6] |
Smith W and Todorov I T 2006 Molecular Simulation 32 935
|
[7] |
Bowers K, Chow E, Xu H, et al. 2006 Proceedings of the ACM/IEEE (2006), pp. 43-43
|
[8] |
Mackerell A D, Wiorkiewicz-Kuczera J and Karplus M 1995 J. Am. Chem. Soc. 117 11946
|
[9] |
Mackerell A D 2004 J. Comput. Chem. 25 1584
|
[10] |
Vanommeslaeghe K, Hatcher E, Acharya C, et al. 2010 J. Comput. Chem. 31 671
|
[11] |
Wang J, Wolf R M, Caldwell J W, Kollman P A and Case D A 2004 J. Comput. Chem. 25 1157
|
[12] |
Yang L, Tan C H, Hsieh M J, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman P A and Luo R 2006 J. Phys. Chem. B 110 13166
|
[13] |
Jorgensen W L, Maxwell D S and Tirado-Rives J 1996 J. Am. Chem. Soc. 118 11225
|
[14] |
Kaminski G and Jorgensen W L 1996 J. Chem. Phys. 100 18010
|
[15] |
Kaminski G A, Friesner R A, Tirado-Rives J and Jorgensen W L 2001 J. Phys. Chem. B 105 6474
|
[16] |
Shivakumar D, Harder E, Damm W, Friesner R A and Sherman W 2012 J. Chem. Theor. Comput. 8 2553
|
[17] |
Chen S, Yi S, Gao W, Zuo C and Hu Z 2015 J. Comput. Chem. 36 376
|
[18] |
York D M, Yang W, Lee H, Darden T and Pedersen L G 1995 J. Am. Chem. Soc. 117 5001
|
[19] |
York D M, Darden T A and Pedersen L G 1993 J. Chem. Phys. 99 8345
|
[20] |
Sagui C and Darden T A 1999 Ann. Rev. Biophys. Biomol. Struc. 28 155
|
[21] |
Huang Y K, Liu X H, Li S and Yan T Y 2016 Chin. Phys. B 25 016801
|
[22] |
Wu T M, Wang T J, Chen X, Fang B, Zhang R T and Zhuang W 2016 Chin. Phys. B 25 018701
|
[23] |
Wang Y 2009 J. Phys. Chem. B 113 11
|
[24] |
Shi R and Yanting W 2013 J. Phys. Chem. B 117 5102
|
[25] |
Ren G, Shi R and Wang Y 2014 J. Phys. Chem. B 118 4404
|
[26] |
Ren G and Wang Y T 2015 Chin. Phys. B 24 126402
|
[27] |
Liu Z R, Wu J and Duan W 2004 Phys. Rev. B 69 085117
|
[28] |
Holm C 2004 “Efficient Methods for Long Range Interactions in Periodic Geometries Plus One Application”, Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, Vol. 23
|
[29] |
Cisneros G A, Karttunen M, Ren P and Sagui C 2014 Chem. Rev. 114 779
|
[30] |
Ewald P P 1921 Ann. Phys. Leipzig 64 253
|
[31] |
Weeks J D 2002 Ann. Rev. Phys. Chem. 53 533
|
[32] |
Rodgers J M and Weeks J D 2008 Proc. Natl. Acad. Sci. USA 105 19136
|
[33] |
Hu Z and Weeks J D 2010 Phys. Rev. Lett. 105 140602
|
[34] |
Rodgers J M, Hu Z and Weeks J D 2011 Mol. Phys. 109 1195
|
[35] |
Hu Z 2014 Chem. Commun. 50 14397
|
[36] |
Pan C and Hu Z 2014 J. Chem. Theor. Comput. 10 534
|
[37] |
Hu Z 2014 J. Chem. Theor. Comput. 10 5254
|
[38] |
Pan C and Hu Z 2015 Sci. China: Chemistry 58 1044
|
[39] |
Schreiber H and Steinhauser O 1992 Biochemistry 31 5856
|
[40] |
Mombelli E, Morris R, Taylor W and Fraternali F 2003 Biophys. J. 84 1507
|
[41] |
Soare C M, Teixeira V H and Baptista A M 2003 Biophys. J. 84 1628
|
[42] |
Allen M P and Tildesley D J 1987 Computer Simulation of Liquids (New York: Oxford University Press)
|
[43] |
Yonetani Y 2005 Chem. Phys. Lett. 406 49
|
[44] |
van der Spoel D and van Maaren P J 2006 J. Chem. Theor. Comput. 2 1
|
[45] |
Darden T, York D and Pedersen L 1993 J. Chem. Phys. 98 10089
|
[46] |
Essmann U, Perera L, Berkowitz M L, Darden T, Lee H and Pedersen L G 1995 J. Chem. Phys. 103 8577
|
[47] |
Deserno M and Holm C 1998 J. Chem. Phys. 109 7678
|
[48] |
Hockney R and Eastwood J 1981 Computer Simulation Using Particles (New York: McGraw-Hill)
|
[49] |
Wolf S P D, Keblinski P and Eggebrecht J 1999 J. Chem. Phys. 110 8254
|
[50] |
Schulz R, Lindner B, Petridis L and Smith J C 2009 J. Chem. Theor. Comput. 5 2798
|
[51] |
Giese T J, Panteva M T, Chen H and York D M 2015 J. Chem. Theor. Comput. 11 436
|
[52] |
Smith P E and Pettitt B M 1996 J. Chem. Phys. 105 4289
|
[53] |
Hummer G, Pratt L R and Garca A E 1997 J. Chem. Phys. 107 9275
|
[54] |
Figueirido F, Del Buono G S and Levy R M 1997 J. Phys. Chem. B 101 5622
|
[55] |
Hunenberger P H and McCammon J A 1999 J. Chem. Phys. 110 1856
|
[56] |
Ekimoto T, Matubayasi N and Ikeguchi M 2015 J. Chem. Theor. Comput. 11 215
|
[57] |
Bogusz S, Cheatham T E and Brooks B R 1998 J. Chem. Phys. 108 7070
|
[58] |
Hummer G, Pratt L R and Garca A E 1996 J. Phys. Chem. 100 1206
|
[59] |
Weeks J D, Katsov K and Vollmayr K 1998 Phys. Rev. Lett. 81 4400
|
[60] |
Kadanoff L P 2000 Statistical Physics (Singapore: World Scientific)
|
[61] |
Chen Y G, Kaur C and Weeks J D 2004 J. Phys. Chem. B 108 19874
|
[62] |
Rodgers J M, Kaur C, Chen Y G and Weeks J D 2006 Phys. Rev. Lett. 97 097801
|
[63] |
Chen Y G and Weeks J D 2006 Proc. Natl. Acad. Sci. USA 103 7560
|
[64] |
Denesyuk N and Weeks J D 2008 J. Chem. Phys. 128 124109
|
[65] |
Katsov K and Weeks J D 2001 Phys. Rev. Lett. 86 440
|