Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born

Journal of Chemical Theory and Computation - Tập 8 Số 5 - Trang 1542-1555 - 2012
Andreas W. Götz1, Mark J. Williamson1, Dongyan Xu1, Duncan Poole2, Scott Le Grand2, Ross C. Walker3,1
1San Diego#R#Supercomputer Center, University of California San Diego, 9500 Gilman Drive#R#MC0505, La Jolla, California 92093, United States
2NVIDIA Corporation, 2701 San Tomas Expressway, Santa Clara, California 95050, United#R#States
3Department of Chemistry and Biochemistry, University of California San Diego, 9500 Gilman Drive MC0505, La Jolla, California 92093, United States

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McCammon J. A., 1977, Nature, 267, 585, 10.1038/267585a0

Duan Y., 1998, Science, 282, 740, 10.1126/science.282.5389.740

Yeh I.-C., 2002, J. Am. Chem. Soc., 124, 6563, 10.1021/ja025789n

Klepeis J. L., 2009, Curr. Opin. Struct. Biol., 19, 120, 10.1016/j.sbi.2009.03.004

Sanbonmatsu K. Y., 2005, Proc. Nat. Acad. Sci. U. S. A., 102, 16854, 10.1073/pnas.0503456102

Freddolino P. L., 2006, Structure, 14, 437, 10.1016/j.str.2005.11.014

Bakker A. F., 1990, J. Comput. Phys., 90, 313, 10.1016/0021-9991(90)90169-2

Fine R., 1991, Proteins: Struct., Funct., Genet., 11, 242, 10.1002/prot.340110403

Susukita R., 2003, Comput. Phys. Commun., 155, 115, 10.1016/S0010-4655(03)00349-7

Shaw D. E., 2008, Commun. ACM, 51, 91, 10.1145/1364782.1364802

Götz A. W., 2010, Annual Reports in Computational Chemistry, 6, 21

Xu D., 2010, Annual Reports in Computational Chemistry, 6, 21

Götz, A. W.; Salomon-Ferrer, R.; Poole, D.; Le Grand, S.; Walker, R. C.Manuscript in preparation.

Phillips J. C., 2008, SC ’08: Proceedings of the 2008 ACM/IEEE Conference on Suprcomputing, 1

Friedrichs M. S., 2009, J. Comput. Chem., 30, 864, 10.1002/jcc.21209

Eastman P., 2010, J. Comput. Chem., 31, 1268, 10.1002/jcc.21413

Harvey M. J., 2009, J. Chem. Theory Comput., 5, 1632, 10.1021/ct9000685

Harvey M. J., 2009, J. Chem. Theory Comput., 5, 2371, 10.1021/ct900275y

10.1109/HPCS.2010.5547149

Brown W. M., 2011, Comput. Phys. Commun., 182, 898, 10.1016/j.cpc.2010.12.021

Cornell W. D., 1995, J. Am. Chem. Soc., 117, 5179, 10.1021/ja00124a002

MacKerell A. D., 1998, J. Phys. Chem. B, 102, 3586, 10.1021/jp973084f

Case D. A., 2010, AMBER 11

Case D. A., 2005, J. Comput. Chem., 26, 1668, 10.1002/jcc.20290

Stone J. E., 2007, J. Comput. Chem., 28, 2618, 10.1002/jcc.20829

Data have been obtained from Intel’s Web page.http://ark.intel.com(accessed September 28, 2011) .

Private communication with Mark Berger (NVIDIA), September 28, 2011.

Kirk D. B., 2010, Programming Massively Parallel Processors

Interface, 2009, MPI: A Message-passing Interface Standard

Mellanox: NVIDIA GPUDirect technology – accelerating GPU-based systems.http://www.mellanox.com/pdf/whitepapers/TB_GPU_Direct.pdf(accessed March 13, 2012) .

Knizia G., 2011, J. Chem. Theory Comput., 7, 2387, 10.1021/ct200239p

Buck L., 2004, ACM Trans. Graph., 23, 777, 10.1145/1015706.1015800

Tsuchiyama R., 2010, The OpenCL Programming Book

Case D. A., 2008, AMBER 10

NVIDIA, CUDA API reference manual.http://developer.download.nvidia.com/compute/DevZone/docs/html/C/doc/CUDA_Toolkit_Reference_Manual.pdf(accessed March 14, 2012) .

The Portland Group, PGI CUDA-X86.http://www.pgroup.com/resources/cuda-x86.htm(accessed March 14, 2012) .

Hawkins G. D., 1996, J. Phys. Chem., 100, 19824, 10.1021/jp961710n

Tsui V., 2001, Biopolymers: Nucleic Acid. Sci., 56, 275, 10.1002/1097-0282(2000)56:4<275::AID-BIP10024>3.0.CO;2-E

Onufriev A., 2000, J. Phys. Chem. B, 104, 3712, 10.1021/jp994072s

Onufriev A., 2004, Proteins, 55, 383, 10.1002/prot.20033

Mongan J., 2007, J. Chem. Theory Comput., 3, 156, 10.1021/ct600085e

Sigalov G., 2006, J. Chem. Phys., 124, 124902, 10.1063/1.2177251

Berendsen H. J. C., 1984, J. Chem. Phys., 81, 3684, 10.1063/1.448118

Andersen H. C., 1980, J. Chem. Phys., 72, 2384, 10.1063/1.439486

Loncharich R. J., 1992, Biopolymers, 32, 523, 10.1002/bip.360320508

Ryckaert J.-P., 1977, J. Comput. Phys., 23, 327, 10.1016/0021-9991(77)90098-5

Miyamoto S., 1992, J. Comput. Chem., 13, 952, 10.1002/jcc.540130805

Hornak V., 2006, Proteins, 65, 712, 10.1002/prot.21123

MacKerell A. D., 2004, J. Comput. Chem., 25, 1400, 10.1002/jcc.20065

Bowers K. J., 2006, Proceedings of the 2006 ACM/IEEE conference on Supercomputing

Walker, R. C.Manuscript in preparation.

Simmerling C., 2002, J. Am. Chem. Soc., 124, 11258, 10.1021/ja0273851

Vijaykumar S., 1985, Proc. Natl. Acad. Sci. U. S. A., 82, 3582, 10.1073/pnas.82.11.3582

Vijaykumar S., 1987, J. Mol. Bio., 194, 531, 10.1016/0022-2836(87)90679-6

The patches can be obtained from following Web page:http://ambermd.org/bugfixes.html(accessed March 13, 2012) .

Karplus M., 2005, Proc. Natl. Acad. Sci. U. S. A., 102, 6679, 10.1073/pnas.0408930102

Maragakis P., 2008, J. Phys. Chem. B, 112, 6155, 10.1021/jp077018h

Koller A. N., 2008, Biophys. J. Lett., 95, L04, 10.1529/biophysj.108.132811

Showalter S. A., 2007, J. Am. Chem. Soc., 129, 4158, 10.1021/ja070658d

Lange O. F., 2010, Biophys. J., 99, 647, 10.1016/j.bpj.2010.04.062

Crighton T. E., 1993, Proteins: Structures and Molecular Properties, 2

Alonso D. O., 1998, Protein Sci., 7, 860, 10.1002/pro.5560070404