mmuecke's molecular_dynamics [22 articles] Export

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	How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines [My Copy] The Journal of Chemical Physics, Vol. 109, No. 18. (1998), pp. 7678-7693. by Markus Deserno, Christian Holm posted to molecular_dynamics charmm by mmuecke on 2009-08-14 08:41:40 as along with 1 person stephenbond
	How to mesh up Ewald sums. II. An accurate error estimate for the particle--particle--particle-mesh algorithm [My Copy] The Journal of Chemical Physics, Vol. 109, No. 18. (1998), pp. 7694-7701. by Markus Deserno, Christian Holm posted to molecular_dynamics error_analysis charmm by mmuecke on 2009-08-14 08:38:56 as along with 1 person stephenbond
	The Amber biomolecular simulation programs. [My Copy] Journal of computational chemistry, Vol. 26, No. 16. (December 2005), pp. 1668-1688. by D. A. Case, T. E. Cheatham, T. Darden, et al.H. Gohlke, R. Luo, K. M. Merz, A. Onufriev, C. Simmerling, B. Wang, R. J. Woods posted to charmm molecular_dynamics by mmuecke on 2009-08-11 11:19:47 as along with 18 people and 3 groups krapnik csrocha nickolay flbarroso charris5 pavanghatty tahereh62 lna jwm ttjoseph xdeupi tovrstra bilab RamuAnandakrishnan IrinaMoreira adilson_mohr mikaellund gisle Radiation_Damage Stressosome LabCompMed
	ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale [My Copy] Journal of Chemical Theory and Computation, Vol. 5, No. 6. (9 June 2009), pp. 1632-1639. by M. J. Harvey, G. Giupponi, G. De Fabritiis posted to charmm gpu molecular_dynamics by mmuecke on 2009-06-30 16:22:21 as along with 4 people and 1 group qshao jmccammon r2s2 ibuch McCammon
	CHARMM: The biomolecular simulation program [My Copy] Journal of Computational Chemistry, Vol. 30, No. 10. (30 July 2009), pp. 1545-1614. by B. R. R. Brooks, C. L. L. Brooks, A. D. D. Mackerell, et al.L. Nilsson, R. J. J. Petrella, B. Roux, Y. Won, G. Archontis, C. Bartels, S. Boresch, A. Caflisch, L. Caves, Q. Cui, A. R. R. Dinner, M. Feig, S. Fischer, J. Gao, M. Hodoscek, W. Im, K. Kuczera, T. Lazaridis, J. Ma, V. Ovchinnikov, E. Paci, R. W. W. Pastor, C. B. B. Post, J. Z. Z. Pu, M. Schaefer, B. Tidor, R. M. M. Venable, H. L. L. Woodcock, X. Wu, W. Yang, D. M. M. York, M. Karplus posted to charmm molecular_dynamics by mmuecke on 2009-06-29 13:46:46 as along with 8 people and 1 group rodrigofaccioli medic0747 flbarroso jrperillaj xavierprat saravan sobolevnrm dimka baker-group
	Performance characterization of a molecular dynamics code on PC clusters: is there any easy parallelism in CHARMM? [My Copy] Parallel and Distributed Processing Symposium., Proceedings International, IPDPS 2002, Abstracts and CD-ROM In Parallel and Distributed Processing Symposium., Proceedings International, IPDPS 2002, Abstracts and CD-ROM (2002), pp. 30-37. by M. Taufer, E. Perathoner, A. Cavalli, A. Caflisch, T. Stricker posted to charmm molecular_dynamics by mmuecke on 2009-06-26 13:15:51 as
	Scalable algorithms for molecular dynamics simulations on commodity clusters [My Copy] In SC '06: Proceedings of the 2006 ACM/IEEE conference on Supercomputing (2006) by Kevin J. Bowers, Edmond Chow, Huafeng Xu, et al.Ron O. Dror, Michael P. Eastwood, Brent A. Gregersen, John L. Klepeis, Istvan Kolossvary, Mark A. Moraes, Federico D. Sacerdoti, John K. Salmon, Yibing Shan, David E. Shaw posted to high-performance_computing molecular_dynamics by mmuecke on 2009-06-25 12:42:06 as along with 2 people r2s2 GermanErlenkamp
	Performance characteristics of biomolecular simulations on high-end systems with multi-core processors [My Copy] Parallel Computing, Vol. 34, No. 11. (November 2008), pp. 640-651. by S. Alam, P. Agarwal, J. Vetter posted to charmm high-performance_computing molecular_dynamics mpi multicore performance_analysis by mmuecke on 2008-11-19 11:50:14 as
	Computing Models for FPGA-Based Accelerators [My Copy] Computing in Science & Engineering In Computing in Science & Engineering, Vol. 10, No. 6. (2008), pp. 35-45. by Martin C. Herbordt, Yongfeng Gu, Tom Vancourt, Josh Model, Bharat Sukhwani, Matt Chiu posted to computer_architecture formal_language_theory fpga fpgasupercomputing language_design molecular_dynamics parallel_programming reconfigurable_computing trends by mmuecke on 2008-11-10 12:52:53 as along with 3 people and 2 groups michael_hliao peskin gferencz rit_ee732 Reconfigurable Computing
	Anton, a special-purpose machine for molecular dynamics simulation [My Copy] Commun. ACM, Vol. 51, No. 7. (July 2008), pp. 91-97. by David E. Shaw, Martin M. Deneroff, Ron O. Dror, et al.Jeffrey S. Kuskin, Richard H. Larson, John K. Salmon, Cliff Young, Brannon Batson, Kevin J. Bowers, Jack C. Chao, Michael P. Eastwood, Joseph Gagliardo, J. P. Grossman, Richard C. Ho, Douglas J. Lerardi, István Kolossváry, John L. Klepeis, Timothy Layman, Christine Mcleavey, Mark A. Moraes, Rolf Mueller, Edward C. Priest, Yibing Shan, Jochen Spengler, Michael Theobald, Brian Towles, Stanley C. Wang posted to molecular_dynamics reconfigurable_platforms vlsi_design by mmuecke on 2008-07-01 13:31:27 as along with 3 people ariels apaydin cwr
	A Survey of FPGAs for Acceleration of High Performance Computing and their Application to Computational Molecular Biology [My Copy] TENCON 2005 2005 IEEE Region 10 In TENCON 2005 2005 IEEE Region 10 (2005), pp. 1-6. by T. Ramdas, G. Egan posted to bioinformatics fpgasupercomputing genomesequencing molecular_docking molecular_dynamics reconfigurable_computing survey trends by mmuecke on 2008-07-01 08:14:09 as along with 1 person and 1 group nevarcds Reconfigurable Computing
	GRAPE-DR: 2-Pflops massively-parallel computer with 512-core, 512-Gflops processor chips for scientific computing [My Copy] In SC '07: Proceedings of the 2007 ACM/IEEE conference on Supercomputing (2007), pp. 1-11. by Junichiro Makino, Kei Hiraki, Mary Inaba posted to computer_architecture high-performance_computing molecular_dynamics by mmuecke on 2008-06-10 10:33:12 as
	Using FPGA Devices to Accelerate Biomolecular Simulations [My Copy] Computer In Computer, Vol. 40, No. 3. (2007), pp. 66-73. by Sadaf R. Alam, Pratul K. Agarwal, Melissa C. Smith, Jeffrey S. Vetter, David Caliga posted to fpgasupercomputing high-performance_computing molecular_dynamics by mmuecke on 2008-05-27 10:39:39 as along with 7 people and 1 group gferencz anallam aso6678 hamish peskin smithmc adilson_mohr rit_ee732
	Accelerating Molecular Dynamics Simulations with Reconfigurable Computers [My Copy] Parallel and Distributed Systems, IEEE Transactions on In Parallel and Distributed Systems, IEEE Transactions on, Vol. 19, No. 6. (2008), pp. 764-778. by R. Scrofano, M. B. Gokhale, F. Trouw, V. K. Prasanna posted to fpgasupercomputing high-performance_computing molecular_dynamics reconfigurable_computing by mmuecke on 2008-05-08 13:57:15 as along with 4 people and 1 group aso6678 anallam gferencz adilson_mohr rit_ee732
	Probing the Applicability of Polarizable Force-Field Molecular Dynamics for Parallel Architectures: A Comparison of Digital MPI with LAM-MPI and MPICH2 [My Copy] Recent Advances in Parallel Virtual Machine and Message Passing Interface (2005), pp. 433-440. by Benjamin Almeida, Reema Mahajan, Dieter Kranzlmüller, Jens Volkert, Siegfried Höfinger posted to case_study high-performance_computing molecular_dynamics mpi parallel_algorithms performance_analysis by mmuecke on 2008-03-14 08:14:18 as
	GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation [My Copy] Journal of Chemical Theory and Computation, Vol. 4, No. 3. (1 March 2008), pp. 435-447. by Berk Hess, Carsten Kutzner, David van der Spoel, Erik Lindahl posted to high-performance_computing molecular_dynamics parallel_algorithms by mmuecke on 2008-02-20 16:18:30 as along with 23 people and 2 groups sunnytov softsimu parnell rabio oteri krapnik robertvacha rodrigofaccioli pavanghatty janneb ZhangYinhe okapi flbarroso marceavi A_Coletta_Thesis choonpeng Lombardo_7 jwm daevans sobolevnrm r2s2 middledomain loison Structural Biology Group TorVergata baker-group
	Detailed analysis of grid-based molecular docking: A case study of CDOCKER - A CHARMm-based MD docking algorithm [My Copy] Journal of Computational Chemistry, Vol. 24, No. 13. (2003), pp. 1549-1562. by Guosheng Wu, Daniel H. Robertson, Charles L. Brooks, Michal Vieth posted to case_study charmm molecular_docking molecular_dynamics by mmuecke on 2008-01-21 14:31:48 as along with 5 people and 1 group oceanwind oteri apostola papatonyhill msuarezdiez Structural Biology Group TorVergata
	CHARMM: A program for macromolecular energy, minimization, and dynamics calculations [My Copy] Journal of Computational Chemistry, Vol. 4, No. 2. (1983), pp. 187-217. by Bernard R. Brooks, Robert E. Bruccoleri, Barry D. Olafson, David J. States, S. Swaminathan, Martin Karplus posted to charmm molecular_dynamics by mmuecke on 2008-01-21 14:29:47 as along with 16 people ubcg08l flbarroso nickolay newton1234 kgutwin r2s2 rpetrenko oceanwind RamuAnandakrishnan tovrstra dfgreen Lombardo_7 dgront rabio saravan gisle
	Grid computing and biomolecular simulation [My Copy] Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 363, No. 1833. (2005), pp. 2017-2035. by Christopher J. Woods, Muan H. Ng, Steven Johnston, et al.Stuart E. Murdock, Bing Wu, Kaihsu Tai, Hans Fangohr, Paul Jeffreys, Simon Cox, Jeremy G. Frey, Mark S. Sansom, Jonathan W. Essex posted to bioinformatics high-performance_computing molecular_docking molecular_dynamics by mmuecke on 2008-01-21 12:27:45 as
	On the performance of molecular dynamics applications on current high-end systems. [My Copy] Philos Transact A Math Phys Eng Sci, Vol. 363, No. 1833. (15 August 2005), pp. 1987-1998. by J. Hein, F. Reid, L. Smith, I. Bush, M. Guest, P. Sherwood posted to charmm high-performance_computing molecular_dynamics survey by mmuecke on 2008-01-21 12:24:25 as along with 1 person hlwoodcock
	A Reconfigurable Load Balancing Architecture for Molecular Dynamics [My Copy] Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International In Parallel and Distributed Processing Symposium, 2007. IPDPS 2007. IEEE International (2007), pp. 1-6. by J. Phillips, M. Areno, C. Rogers, A. Dasu, B. Eames posted to fpga molecular_dynamics by mmuecke on 2007-11-27 00:19:28 as along with 1 person and 1 group gferencz rit_ee732
	Adventures in Improving the Scaling and Accuracy of a Parallel Molecular Dynamics Program [My Copy] J. Supercomput., Vol. 11, No. 3. (1 November 1997), pp. 255-278. by Michael Crowley, Tom Darden, Thomas Cheatham, David Deerfield posted to fft high-performance_computing molecular_dynamics by mmuecke on 2007-10-10 12:55:41 as along with 2 people anallam adilson_mohr

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high-performance_computing	78
fpga	74
hdl	74
floating_point	66
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mpi	61
performance_analysis	52
parallel_programming	49
reconfigurable_computing	41
survey	40
computer_architecture	33
error_analysis	32
fixedpoint	28
fpgas_in_hep	28
vlsi_design	28
fpgasupercomputing	27
functional	26
vhdl	25
dsl	24
language_design	24
matrix	23
mpi_tools	23
trends	23
molecular_dynamics	22
reconfigurable_platforms	20
image_processing	19
compiler_design	18
bioinformatics	17
hdl_tool	17
dfg	16
numa	16
communication_algorithms	15
scientific_publishing	15
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mixed_precision	14
architecture_comparison	13
dsp_on_fpga	13
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charmm	12
formal_language_theory	11
multicore	11
svm	11
fft	10
interval_arithmetic	10
teaching	10
computer_arithmetic	9
performance_modelling	8
signal_processing_theory	8
matrix_sparse	7
molecular_docking	7
parallel_algorithms	7
sopc	7
systemc	7
term_rewriting	7
lhcb	6
lhc_transversefeedbacksystem	6
verification	6
genomesequencing	5
vlsi_design_theory	5
adl	4
benchmark	4
case_study	4
formal_synthesis	4
gpu	4
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infiniband	4
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protein_sequences	4
cell_cpu	3
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quantization_noise	1
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mmuecke's molecular_dynamics [22 articles] Export

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