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Title: Advanced Potential Energy Surfaces for Molecular Simulation

Abstract

Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). Here in this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. Finally, we have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functionalmore » theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.« less

Authors:
 [1];  [2];  [3];  [4];  [5];  [4];  [6];  [7];  [8];  [7];  [9];  [9];  [3];  [4];  [9];  [10];  [11];  [3];  [12];  [13] more »;  [14] « less
  1. Univ. of California, Berkeley, CA (United States). Dept. of Chemical and Biomolecular Engineering
  2. Bates College, Lewiston, ME (United States). Dept. of Mathematics
  3. Univ. of Southampton (United Kingdom). School of Chemistry
  4. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry
  5. Univ. of Southampton (United Kingdom). School of Chemistry; Gdansk Univ. of Technology, Gdansk (Poland). Faculty of Applied Physics and Mathematics
  6. New York Univ. (NYU), NY (United States). Dept. of Chemistry
  7. Rutgers Univ., Piscataway, NJ (United States). Dept. of Chemistry and Chemical Biology
  8. National Inst. of Health (NIH), Bethesda, MD (United States). Lab. of Computational Biology, National Heart, Lung and Blood Inst.
  9. Stanford Univ., CA (United States). Dept. of Chemistry
  10. Washington Univ., St. Louis, MO (United States). Dept. Chemistry
  11. Q-Chem Inc., Pleasanton, CA (United States)
  12. Science and Technology Facilities Council (STFC), Daresbury (United Kingdom). Daresbury Lab.
  13. New York Univ. (NYU), NY (United States). Courant Inst. of Mathematical Science, and Dept. of Chemistry; NYU-ECNU, Center for Computational Chemistry at NYU, Shanghai (China)
  14. Univ. of California, Berkeley, CA (United States). Dept. of Chemistry, Dept. of Chemical and Biomolecular Engineering, and Dept. of Bioengineering
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22), Scientific User Facilities Division (SC-22.3 )
OSTI Identifier:
1478341
Grant/Contract Number:  
AC02-05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry
Additional Journal Information:
Journal Volume: 120; Journal Issue: 37; Journal ID: ISSN 1520-6106
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; 97 MATHEMATICS AND COMPUTING

Citation Formats

Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard T., Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan W., Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris-Kriton, Todorov, Ilian T., Tuckerman, Mark E., and Head-Gordon, Teresa. Advanced Potential Energy Surfaces for Molecular Simulation. United States: N. p., 2016. Web. doi:10.1021/acs.jpcb.6b06414.
Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard T., Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan W., Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris-Kriton, Todorov, Ilian T., Tuckerman, Mark E., & Head-Gordon, Teresa. Advanced Potential Energy Surfaces for Molecular Simulation. United States. https://doi.org/10.1021/acs.jpcb.6b06414
Albaugh, Alex, Boateng, Henry A., Bradshaw, Richard T., Demerdash, Omar N., Dziedzic, Jacek, Mao, Yuezhi, Margul, Daniel T., Swails, Jason, Zeng, Qiao, Case, David A., Eastman, Peter, Wang, Lee-Ping, Essex, Jonathan W., Head-Gordon, Martin, Pande, Vijay S., Ponder, Jay W., Shao, Yihan, Skylaris, Chris-Kriton, Todorov, Ilian T., Tuckerman, Mark E., and Head-Gordon, Teresa. Thu . "Advanced Potential Energy Surfaces for Molecular Simulation". United States. https://doi.org/10.1021/acs.jpcb.6b06414. https://www.osti.gov/servlets/purl/1478341.
@article{osti_1478341,
title = {Advanced Potential Energy Surfaces for Molecular Simulation},
author = {Albaugh, Alex and Boateng, Henry A. and Bradshaw, Richard T. and Demerdash, Omar N. and Dziedzic, Jacek and Mao, Yuezhi and Margul, Daniel T. and Swails, Jason and Zeng, Qiao and Case, David A. and Eastman, Peter and Wang, Lee-Ping and Essex, Jonathan W. and Head-Gordon, Martin and Pande, Vijay S. and Ponder, Jay W. and Shao, Yihan and Skylaris, Chris-Kriton and Todorov, Ilian T. and Tuckerman, Mark E. and Head-Gordon, Teresa},
abstractNote = {Advanced potential energy surfaces are defined as theoretical models that explicitly include many-body effects that transcend the standard fixed-charge, pairwise-additive paradigm typically used in molecular simulation. However, several factors relating to their software implementation have precluded their widespread use in condensed-phase simulations: the computational cost of the theoretical models, a paucity of approximate models and algorithmic improvements that can ameliorate their cost, underdeveloped interfaces and limited dissemination in computational code bases that are widely used in the computational chemistry community, and software implementations that have not kept pace with modern high-performance computing (HPC) architectures, such as multicore CPUs and modern graphics processing units (GPUs). Here in this Feature Article we review recent progress made in these areas, including well-defined polarization approximations and new multipole electrostatic formulations, novel methods for solving the mutual polarization equations and increasing the MD time step, combining linear-scaling electronic structure methods with new QM/MM methods that account for mutual polarization between the two regions, and the greatly improved software deployment of these models and methods onto GPU and CPU hardware platforms. Finally, we have now approached an era where multipole-based polarizable force fields can be routinely used to obtain computational results comparable to state-of-the-art density functional theory while reaching sampling statistics that are acceptable when compared to that obtained from simpler fixed partial charge force fields.},
doi = {10.1021/acs.jpcb.6b06414},
journal = {Journal of Physical Chemistry. B, Condensed Matter, Materials, Surfaces, Interfaces and Biophysical Chemistry},
number = 37,
volume = 120,
place = {United States},
year = {Thu Aug 11 00:00:00 EDT 2016},
month = {Thu Aug 11 00:00:00 EDT 2016}
}

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