CUDA Treecode in Python App for Biomolecular Electrostatics | GTC ...

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BEM discretization12 ⇥ 1(r i )N p⇤j=1⌅⇤⇥ 1⇤n (r j)⌥j14 |r i r | d⌃⇧N p⇤+j=1⌅⇥ 1 (r j )⌥j⇤⇤n⇥1d4 |r i r |⌃⇧=N ck=0q k114⇥|r i r k |N12 ⇤ ⇤ p1(r i )+j=1⌅⇤ 1⌅n (r j) 1 2⌅⌥jV Le|r i r |4⇥|r i⌃⇧r ⇥ | d ⇥N p⇤j=1⌅⇤ 1 (r j )⌥j⌅⌅nK Le|r i r |4⇥|r i r ⇥ |⌃⇧⇥d ⇥=0V YK Yiq k+1q k+2q kiΓj+1Ω 1 , ɛ 1 , φ 1 jq k 1apple 1Ω 2 , ɛ 2 , 2φ I + K Lq 2k 2 1j 12 I K YV L✏ 1✏ 2V Yapple@@n=apple Q06
Solution:L<strong>in</strong>ear algebra turns to N-body.
Page 1: entity Standardst.GTC 2013CUDA tree
Page 4 and 5: Biomolecular Electrostatics:e model
Page 8 and 9: GMRESSaad, Schultz (1986)8
Page 10 and 11: N-body problemr kr i10
Page 12 and 13: Treecodew(x i )=XN kj=1m 0 jG(x i ,
Page 14 and 15: Treecodew(x i ) ⇡PX||k||=01k! Dk
Page 20 and 21: Hardware Acceleration:e treecode on
Page 22 and 23: Treecode on GPU - Results✓ =0.5P
Page 24 and 25: Multi-region models‣ Stern layers
Page 26 and 27: Lysozyme molecule: comparison with
Page 28 and 29: 1HIV protease22
Page 30: PyGBe:1) is code is open (find it o

CUDA Treecode in Python App for Biomolecular Electrostatics | GTC ...

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