-
Notifications
You must be signed in to change notification settings - Fork 0
/
md.bib
140 lines (118 loc) · 3.85 KB
/
md.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
*********** PAPER VIEJOS DE DINAMICA MOLECULAR *********8
@article{mccamm0n1977dynamics,
title={Dynamics of folded proteins},
author={McCamm0n, J Andrew},
journal={Nature},
volume={267},
pages={16},
year={1977}
}
@article{piana2014assessing,
title={Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations},
author={Piana, Stefano and Klepeis, John L and Shaw, David E},
journal={Current opinion in structural biology},
volume={24},
pages={98--105},
year={2014},
publisher={Elsevier}
}
@article{stone2010gpu,
title={GPU-accelerated molecular modeling coming of age},
author={Stone, John E and Hardy, David J and Ufimtsev, Ivan S and Schulten, Klaus},
journal={Journal of Molecular Graphics and Modelling},
volume={29},
number={2},
pages={116--125},
year={2010},
publisher={Elsevier}
}
@article{senn2009qm,
title={QM/MM methods for biomolecular systems},
author={Senn, Hans Martin and Thiel, Walter},
journal={Angewandte Chemie International Edition},
volume={48},
number={7},
pages={1198--1229},
year={2009},
publisher={Wiley Online Library}
}
@article{noid2013perspective,
title={Perspective: coarse-grained models for biomolecular systems},
author={Noid, WG},
journal={The Journal of chemical physics},
volume={139},
number={9},
pages={090901},
year={2013},
publisher={AIP Publishing}
}
@article{friedrichs2009accelerating,
title={Accelerating molecular dynamic simulation on graphics processing units},
author={Friedrichs, Mark S and Eastman, Peter and Vaidyanathan, Vishal and Houston, Mike and Legrand, Scott and Beberg, Adam L and Ensign, Daniel L and Bruns, Christopher M and Pande, Vijay S},
journal={Journal of computational chemistry},
volume={30},
number={6},
pages={864--872},
year={2009},
publisher={Wiley Online Library}
}
@article{tsui2000theory,
title={Theory and applications of the generalized Born solvation model in macromolecular simulations},
author={Tsui, Vickie and Case, David A},
journal={Biopolymers},
volume={56},
number={4},
pages={275--291},
year={2000},
publisher={Wiley Online Library}
}
@article{toukmaji1996ewald,
title={Ewald summation techniques in perspective: a survey},
author={Toukmaji, Abdulnour Y and Board, John A},
journal={Computer Physics Communications},
volume={95},
number={2},
pages={73--92},
year={1996},
publisher={Elsevier}
}
@article{plimpton1995fast,
title={Fast parallel algorithms for short-range molecular dynamics},
author={Plimpton, Steve},
journal={Journal of computational physics},
volume={117},
number={1},
pages={1--19},
year={1995},
publisher={Elsevier}
}
@article{gotz2012routine,
title={Routine microsecond molecular dynamics simulations with AMBER on GPUs. 1. Generalized born},
author={G{\"o}tz, Andreas W and Williamson, Mark J and Xu, Dong and Poole, Duncan and Le Grand, Scott and Walker, Ross C},
journal={Journal of chemical theory and computation},
volume={8},
number={5},
pages={1542--1555},
year={2012},
publisher={ACS Publications}
}
@article{salomon2013routine,
title={Routine microsecond molecular dynamics simulations with AMBER on GPUs. 2. Explicit solvent particle mesh Ewald},
author={Salomon-Ferrer, Romelia and G{\"o}tz, Andreas W and Poole, Duncan and Le Grand, Scott and Walker, Ross C},
journal={Journal of Chemical Theory and Computation},
volume={9},
number={9},
pages={3878--3888},
year={2013},
publisher={ACS Publications}
}
@article{le2013spfp,
title={SPFP: Speed without compromise—A mixed precision model for GPU accelerated molecular dynamics simulations},
author={Le Grand, Scott and G{\"o}tz, Andreas W and Walker, Ross C},
journal={Computer Physics Communications},
volume={184},
number={2},
pages={374--380},
year={2013},
publisher={Elsevier}
}