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 | 1873 | 2020 |
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 | 937 | 2007 |
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 | 510 | 2010 |
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 | 295 | 2010 |
Multilevel summation of electrostatic potentials using graphics processing units DJ Hardy, JE Stone, K Schulten Parallel computing 35 (3), 164-177, 2009 | 168 | 2009 |
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 | 165 | 2008 |
Multiple grid methods for classical molecular dynamics RD Skeel, I Tezcan, DJ Hardy Journal of Computational Chemistry 23 (6), 673-684, 2002 | 162 | 2002 |
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 | 153 | 2021 |
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 | 120 | 1999 |
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 | 95 | 2001 |
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 | 78 | 2016 |
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 | 73 | 2015 |
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 | 73 | 2010 |
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 | 72 | 2009 |
namd User’s Guide M Bhandarkar, R Brunner, C Chipot, A Dalke, S Dixit, P Grayson, ... Urbana 51, 61801, 2003 | 64 | 2003 |
# 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 | 62 | 2023 |
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 | 54 | 2018 |
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 | 44 | 2020 |