TY - JOUR T1 - DASHMM Accelerated Adaptive Fast Multipole Poisson-Boltzmann Solver on Distributed Memory Architecture JO - Communications in Computational Physics VL - 4 SP - 1235 EP - 1258 PY - 2018 DA - 2018/12 SN - 25 DO - http://doi.org/10.4208/cicp.OA-2018-0098 UR - https://global-sci.org/intro/article_detail/cicp/12897.html KW - Poisson-Boltzmann equation, boundary element method, DASHMM, distributed computing. AB -

We present DAFMPB (DASHMM-accelerated Adaptive Fast Multipole Poisson-Boltzmann solver) for rapid evaluation of the electrostatic potentials and forces, and total solvation-free energy in biomolecular systems modeled by the linearized Poisson-Boltzmann (LPB) equation. DAFMPB first reformulates the LPB into a boundary integral equation and then discretizes it using the node-patch scheme [33]. It solves the resulting linear system using GMRES, where it adopts the DASHMM library [14] to accelerate the matrix-vector multiplication in each iteration. DASHMM is built on top of a global address space allowing the user of DAFMPB to operate on both shared and distributed memory computers with modification of their code. This paper is a brief summary of the program, including the algorithm, implementation, installation and usage.