scholarly journals A boundary integral Poisson-Boltzmann solvers package for solvated bimolecular simulations

2015 ◽  
Vol 3 (1) ◽  
Author(s):  
Weihua Geng
Keyword(s):  
Boltzmann Equation ◽  
High Performance ◽  
Numerical Algorithms ◽  
Boundary Integral ◽  
Partial Charges ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
High Performance Computers ◽  
Energy Computation ◽  
A Current

AbstractNumerically solving the Poisson-Boltzmann equation is a challenging task due to the existence of the dielectric interface, singular partial charges representing the biomolecule, discontinuity of the electrostatic field, infinite simulation domains, etc. Boundary integral formulation of the Poisson-Boltzmann equation can circumvent these numerical challenges and meanwhile conveniently use the fast numerical algorithms and the latest high performance computers to achieve combined improvement on both efficiency and accuracy. In the past a few years, we developed several boundary integral Poisson-Boltzmann solvers in pursuing accuracy, efficiency, and the combination of both. In this paper, we summarize the features and functions of these solvers, and give instructions and references for potential users. Meanwhile, we quantitatively report the solvation free energy computation of these boundary integral PB solvers benchmarked with Matched Interface Boundary Poisson-Boltzmann solver (MIBPB), a current 2nd order accurate finite difference Poisson-Boltzmann solver.

scholarly journals A Combined MPI-CUDA Parallel Solution of Linear and Nonlinear Poisson-Boltzmann Equation

2014 ◽  
Vol 2014 ◽  
pp. 1-12 ◽  
Author(s):  
José Colmenares ◽  
Antonella Galizia ◽  
Jesús Ortiz ◽  
Andrea Clematis ◽  
Walter Rocchia
Keyword(s):  
Boltzmann Equation ◽  
High Performance ◽  
Biological Macromolecules ◽  
Computational Power ◽  
Parallel Solution ◽  
Fixed Charges ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation ◽  
Novel Algorithms ◽  
Performance Computing

The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological systems. In the last decades, the amount of data concerning proteins and other biological macromolecules has remarkably increased. To fruitfully exploit these data, a huge computational power is needed as well as software tools capable of exploiting it. It is therefore necessary to move towards high performance computing and to develop proper parallel implementations of already existing and of novel algorithms. Nowadays, workstations can provide an amazing computational power: up to 10 TFLOPS on a single machine equipped with multiple CPUs and accelerators such as Intel Xeon Phi or GPU devices. The actual obstacle to the full exploitation of modern heterogeneous resources is efficient parallel coding and porting of software on such architectures. In this paper, we propose the implementation of a full Poisson-Boltzmann solver based on a finite-difference scheme using different and combined parallel schemes and in particular a mixed MPI-CUDA implementation. Results show great speedups when using the two schemes, achieving an 18.9x speedup using three GPUs.

scholarly journals A Poisson-Boltzmann Equation Test Model for Protein in Spherical Solute Region and its Applications

2014 ◽  
Vol 2 (1) ◽  
pp. 86-97 ◽  
Author(s):  
Dexuan Xie ◽  
Yi Jiang ◽  
Jinyong Ying
Keyword(s):  
Finite Element ◽  
Boltzmann Equation ◽  
Continuum Model ◽  
Numerical Algorithms ◽  
Implicit Solvent ◽  
Numerical Comparison ◽  
Test Model ◽  
Comparison Study ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation

Abstract The Poisson-Boltzmann equation (PBE) is one important implicit solvent continuum model for calculating electrostatics of protein in ionic solvent. Several numerical algorithms and program packages have been developed but verification and comparison between them remains an interesting topic. In this paper, a PBE test model is presented for a protein in a spherical solute region, along with its analytical solution. It is then used to verify a PBE finite element solver and applied to a numerical comparison study between a finite element solver and a finite difference solver. Such a study demonstrates the importance of retaining the interface conditions in the development of PBE solvers.

scholarly journals Numerical algorithms for high-performance computational science

2020 ◽  
Vol 378 (2166) ◽  
pp. 20190066 ◽  
Author(s):  
Jack Dongarra ◽  
Laura Grigori ◽  
Nicholas J. Higham
Keyword(s):  
High Performance ◽  
Numerical Algorithms ◽  
Computational Science ◽  
Floating Point ◽  
Important Criterion ◽  
Data Movement ◽  
Floating Point Arithmetic ◽  
High Performance Computers ◽  
Point Arithmetic ◽  
Speed And Accuracy

A number of features of today’s high-performance computers make it challenging to exploit these machines fully for computational science. These include increasing core counts but stagnant clock frequencies; the high cost of data movement; use of accelerators (GPUs, FPGAs, coprocessors), making architectures increasingly heterogeneous; and multi- ple precisions of floating-point arithmetic, including half-precision. Moreover, as well as maximizing speed and accuracy, minimizing energy consumption is an important criterion. New generations of algorithms are needed to tackle these challenges. We discuss some approaches that we can take to develop numerical algorithms for high-performance computational science, with a view to exploiting the next generation of supercomputers. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

scholarly journals Monte Carlo methods for linear and non-linear Poisson-Boltzmann equation

2015 ◽  
Vol 48 ◽  
pp. 420-446 ◽  
Author(s):  
Mireille Bossy ◽  
Nicolas Champagnat ◽  
Hélène Leman ◽  
Sylvain Maire ◽  
Laurent Violeau ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Boltzmann Equation ◽  
Monte Carlo Methods ◽  
Non Linear ◽  
Poisson Boltzmann ◽  
Poisson Boltzmann Equation
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