Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code
نویسندگان
چکیده
In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and angles. This allows us to extend length of interval therefore range physical phenomena that afford simulate. We examine existing algorithms software for solving nonlinear constraint equations in parallel explain why it is necessary advance state-of-the-art. present ILVES-PC, a new algorithm proteins accurately efficiently. It solves same system differential algebraic as celebrated SHAKE algorithm, but ILVES-PC using Newton's method rather than Gauss-Seidel method. Moreover, linear systems specialized solver exploits structure protein. rapidly solve hardware will allow. The run-time proportional number constraints. have integrated into GROMACS simulated different sizes. Compared with SHAKE, achieved speedups up 4.9× single-threaded executions 76× shared-memory multi-threaded executions. more accurate P-LINCS algorithm. Our work proof-of-concept utility designed specifically simulation polymers.
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ژورنال
عنوان ژورنال: Computer Physics Communications
سال: 2023
ISSN: ['1879-2944', '0010-4655']
DOI: https://doi.org/10.1016/j.cpc.2023.108742