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David J. Hardy
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Scalable molecular dynamics on CPU and GPU architectures with NAMD
JC Phillips, DJ Hardy, JDC Maia, JE Stone, JV Ribeiro, RC Bernardi, ...
The Journal of chemical physics 153 (4), 2020
17712020
Accelerating molecular modeling applications with graphics processors
JE Stone, JC Phillips, PL Freddolino, DJ Hardy, LG Trabuco, K Schulten
Journal of Computational Chemistry 28 (16), 2618-2640, 2007
9312007
GPU-accelerated molecular modeling coming of age
JE Stone, DJ Hardy, IS Ufimtsev, K Schulten
Journal of Molecular Graphics and Modelling 29 (2), 116-125, 2010
5062010
High-performance scalable molecular dynamics simulations of a polarizable force field based on classical Drude oscillators in NAMD
W Jiang, DJ Hardy, JC Phillips, AD MacKerell Jr, K Schulten, B Roux
Journal of Physical Chemistry Letters 2 (2), 87-92, 2010
2902010
Multilevel summation of electrostatic potentials using graphics processing units
DJ Hardy, JE Stone, K Schulten
Parallel computing 35 (3), 164-177, 2009
1672009
GPU acceleration of cutoff pair potentials for molecular modeling applications
CI Rodrigues, DJ Hardy, JE Stone, K Schulten, WMW Hwu
Proceedings of the 5th Conference on Computing Frontiers, 273-282, 2008
1622008
Multiple grid methods for classical molecular dynamics
RD Skeel, I Tezcan, DJ Hardy
Journal of Computational Chemistry 23 (6), 673-684, 2002
1622002
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics
L Casalino, AC Dommer, Z Gaieb, EP Barros, T Sztain, SH Ahn, A Trifan, ...
The International Journal of High Performance Computing Applications 35 (5 …, 2021
1482021
Deza graphs: A generalization of strongly regular graph
M Erickson, S Fernando, WH Haemers, D Hardy, J Hemmeter
Journal of Combinatorial Design 7, 395-405, 1999
1201999
GPU algorithms for molecular modeling
JE Stone, DJ Hardy, B Isralewitz, K Schulten
Scientific Computing with Multicore and Accelerators, 351-371, 2011
106*2011
Practical construction of modified Hamiltonians
RD Skeel, DJ Hardy
SIAM Journal on Scientific Computing 23 (4), 1172-1188, 2001
942001
Scientific Computing with Multicore and Accelerators
W Alvaro, J Kurzak, J Dongarra, S Tomov, R Nath, S Williams, N Bell, ...
Chapman & Hall/CRC Press, 2011
92*2011
TopoGromacs: Automated topology conversion from CHARMM to GROMACS within VMD
JV Vermaas, DJ Hardy, JE Stone, E Tajkhorshid, A Kohlmeyer
Journal of chemical information and modeling 56 (6), 1112-1116, 2016
732016
Molecular dynamics simulations suggest that electrostatic funnel directs binding of Tamiflu to influenza N1 neuraminidases
L Le, EH Lee, DJ Hardy, TN Truong, K Schulten
PLoS Computational Biology 6 (9), e1000939, 2010
722010
Multilevel summation method for electrostatic force evaluation
DJ Hardy, Z Wu, JC Phillips, JE Stone, RD Skeel, K Schulten
Journal of Chemical Theory and Computation 11 (2), 766-779, 2015
712015
High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs
JE Stone, J Saam, DJ Hardy, KL Vandivort, WW Hwu, K Schulten
Proceedings of 2nd workshop on general purpose processing on graphics …, 2009
712009
namd User˘s Guide
M Bhandarkar, R Brunner, C Chipot, A Dalke, S Dixit, P Grayson, ...
Urbana 51, 61801, 2003
642003
# COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol
A Dommer, L Casalino, F Kearns, M Rosenfeld, N Wauer, SH Ahn, ...
The international journal of high performance computing applications 37 (1 …, 2023
522023
Scalable molecular dynamics with NAMD on the summit system
B Acun, DJ Hardy, LV Kale, K Li, JC Phillips, JE Stone
IBM journal of research and development 62 (6), 4: 1-4: 9, 2018
522018
Boosting free-energy perturbation calculations with GPU-accelerated NAMD
H Chen, JDC Maia, BK Radak, DJ Hardy, W Cai, C Chipot, E Tajkhorshid
Journal of chemical information and modeling 60 (11), 5301-5307, 2020
432020
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Articles 1–20