A geometric initial guess for localized electronic orbitals in modular biological systems

Technical Report · Mon Sep 11 00:00:00 EDT 2017

DOI:https://doi.org/10.2172/1393357· OSTI ID:1393357

Beckman, P. G. ^[1]; Fattebert, J. L. ^[2]; Lau, E. Y. ^[3]; Osei-Kuffuor, D. ^[3]

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1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Univ. of Chicago, IL (United States)
2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

Recent first-principles molecular dynamics algorithms using localized electronic orbitals have achieved O(N) complexity and controlled accuracy in simulating systems with finite band gaps. However, accurately deter- mining the centers of these localized orbitals during simulation setup may require O(N³) operations, which is computationally infeasible for many biological systems. We present an O(N) approach for approximating orbital centers in proteins, DNA, and RNA which uses non-localized solutions for a set of fixed-size subproblems to create a set of geometric maps applicable to larger systems. This scalable approach, used as an initial guess in the O(N) first-principles molecular dynamics code MGmol, facilitates first-principles simulations in biological systems of sizes which were previously impossible.

• Research Organization: Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
• Sponsoring Organization: USDOE
• DOE Contract Number: AC52-07NA27344
• OSTI ID: 1393357
• Report Number(s): LLNL-TR-738503
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
74 ATOMIC AND MOLECULAR PHYSICS
97 MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE