Molecular dynamics and quantum chemistry from atmospheric chemistry to biomolecules
Andreas Goetz, University of California, San Diego
0000-0002-8048-6906
ACCESS Allocation Request CHE130010
| Past CoPI: | Andreas Goetz | University of California, San Diego |
| Abstract: | I request computer time for continued support of simulations and software development for research projects that are funded through four NSF awards and one NIH award. No other compute resources are available to perform the required simulations for these awards. 1) Density functional theory (DFT) based quantum mechanical (QM) and mixed QM and classical molecular mechanical (QM/MM) molecular dynamics (MD) simulations of cytochrome c oxidase (CcO). Based on results obtained with the previous allocation, I will continue DFT calculations of the reaction mechanism in CcO, which couples oxygen reduction within its Fe–Cu dinuclear active site complex (DNC) to proton pumping across the cell membrane. I will compute thermochemical corrections within the harmonic approximation to obtain accurate energetics of different protonation states and tautomers over the catalytic cycle. Classical constant pH MD simulations and (adaptive) QM/MM MD simulations will give new insight into proton transport mechanisms above the DNC and elucidate the interplay between redox states, protonation states, conformational changes as they relate to proton expulsion mechanisms via the water channels that we have identified with previous simulations. 2) Development of highly accurate many-body potentials based on coupled cluster reference data for molecular simulations of atmospherically relevant molecules that are studied within the NSF Center for Aerosol Impacts on Chemistry of the Environment (CAICE). In particular, in the current funding period this pertains to potentials for dinitrogenpentoxide and hypohalous acids in combination with water. These potentials will be employed to the computational modeling of structural, energetic and thermodynamics properties of these gas pollutants in water clusters to connect to experimental measurements in the center. We will also determine the potential of mean force for the solvation in bulk water with the main goal to determine solubilities that cannot be measured with current experimental techniques but are of relevance for atmospheric and global chemical transport models. 3) Continued development of methods and software for DFT calculations, (adaptive) QM/MM molecular dynamics simulations, and MD simulations with many-body potentials. | |
Allocations:
| 2019 | PSC Bridges-2 Regular Memory (PSC Bridges-2 RM) | 58,631.0 Core-hours |
| 2019 | PSC Bridges-2 Storage (PSC Ocean) | 500.0 GB |
| 2019 | PSC Regular Memory (Bridges) | 76,004.06 SUs |
| 2019 | SDSC Comet GPU Nodes (Comet GPU) | 13,578.0 GPU Hours |
| 2019 | SDSC Dell Cluster with Intel Haswell Processors (Comet) | 272,030.0 SUs |
| 2019 | SDSC Expanse CPU | 322,362.0 Core-hours |
| 2019 | SDSC Expanse GPU | 5,136.0 GPU Hours |
| 2019 | SDSC Expanse Projects Storage | 1,000.0 GB |
| 2019 | TACC Dell/Intel Knights Landing, Skylake System (Stampede2) | 13,675.0 Node Hours |
| 2019 | TACC Long-term tape Archival Storage (Ranch) | 500.0 GB |
| The estimated value of these awarded resources is $17,790.72. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources. | ||
| 2017 | PSC Regular Memory (Bridges) | 286,062.0 SUs |
| 2017 | PSC Storage (Bridges Pylon) | 500.0 GB |
| 2017 | SDSC Comet GPU Nodes (Comet GPU) | 30,103.0 GPU Hours |
| 2017 | SDSC Dell Cluster with Intel Haswell Processors (Comet) | 32,585.0 SUs |
| 2017 | SDSC Medium-term disk storage (Data Oasis) | 500.0 GB |
| 2017 | TACC Dell/Intel Knights Landing, Skylake System (Stampede2) | 3,258.0 Node Hours |
| 2017 | TACC HP/NVIDIA Interactive Visualization and Data Analytics System (Maverick) | 95,881.0 SUs |
| 2017 | TACC Long-term tape Archival Storage (Ranch) | 500.0 GB |
| The estimated value of these awarded resources is $14,510.52. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources. | ||
| 2016 | PSC Regular Memory (Bridges) | 50,000.0 SUs |
| 2016 | PSC Storage (Bridges Pylon) | 500.0 GB |
| 2016 | SDSC Appro with Intel Sandy Bridge Cluster (Gordon Compute Cluster) | 106,995.0 SUs |
| 2016 | SDSC Comet GPU Nodes (Comet GPU) | 288.0 GPU Hours |
| 2016 | SDSC Dell Cluster with Intel Haswell Processors (Comet) | 261,867.0 SUs |
| 2016 | SDSC Medium-term disk storage (Data Oasis) | 500.0 GB |
| 2016 | TACC Dell PowerEdge C8220 Cluster with Intel Xeon Phi coprocessors (Stampede) | 114,125.0 Core-hours |
| 2016 | TACC Dell/Intel Knights Landing, Skylake System (Stampede2) | 970.0 Node Hours |
| 2016 | TACC Long-term tape Archival Storage (Ranch) | 500.0 GB |
| The estimated value of these awarded resources is $14,663.90. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources. | ||
| 2015 | SDSC Appro with Intel Sandy Bridge Cluster (Gordon Compute Cluster) | 122,462.0 SUs |
| 2015 | SDSC Dell Cluster with Intel Haswell Processors (Comet) | 220,431.0 SUs |
| 2015 | SDSC Medium-term disk storage (Data Oasis) | 512.0 GB |
| 2015 | TACC Dell PowerEdge C8220 Cluster with Intel Xeon Phi coprocessors (Stampede) | 212,985.0 Core-hours |
| 2015 | TACC Long-term tape Archival Storage (Ranch) | 500.0 GB |
| The estimated value of these awarded resources is $15,225.18. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources. | ||
| 2013 | SDSC Appro with Intel Sandy Bridge Cluster (Gordon Compute Cluster) | 1,500,000.0 SUs |
| 2013 | TACC Dell PowerEdge C8220 Cluster with Intel Xeon Phi coprocessors (Stampede) | 455,000.0 Core-hours |
| The estimated value of these awarded resources is $107,644.82. The allocation of these resources represents a considerable investment by the NSF in advanced computing infrastructure for the U.S. The dollar value of the allocation is estimated from the NSF awards supporting the allocated resources. | ||
Other Titles:
Click to show/hide prior titles »| Molecular dynamics and quantum chemistry of biomolecules and materials |
| QM and QM/MM simulations of biomolecular systems |