Molecular dynamics simulations allow us to study the behavior of complex biomolecular systems by modeling the pairwise interaction forces between all atoms. Molecular systems are subject to slowly decaying electrostatic potentials, which turn molecular dynamics into an n-body problem. In this paper, we present a parallel and scalable solution to compute long-range molecular forces, based […]

September 15, 2014 by hgpu

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 structural data concerning proteins and other […]

May 21, 2014 by hgpu

This document proposes an alternative method for the comparison of molecular electrostatic potential (MEP), based on parallel computing algorithms on graphics cards using NVIDIA CUDA platform and kernel methods for pattern recognition. The proposed solution optimizes the construction process of a particular representation of MEP, presents options for improving this representation, and offers 11 kernel […]

December 29, 2011 by hgpu

We describe a C++ library for electromagnetics based on the Finite-Difference Time-Domain method for transient analysis, and the Finite Element Method for modal analysis. Both methods share the same core and also both methods are optimized for CPU and GPU computing. The FEM method is applied for solving Laplace’s equation and analyzes the relation between […]

December 13, 2011 by hgpu

We present results of molecular dynamics simulations of fully hydrated DMPC bilayers performed on graphics processing units (GPUs) using current state-of-the-art non-polarizable force fields and a local GPU-enabled molecular dynamics code named FEN ZI. We treat the conditionally convergent electrostatic interaction energy exactly using the particle mesh Ewald method (PME) for solution of Poisson’s Equation […]

August 8, 2011 by hgpu

Research efforts to analyze biomolecular properties contribute towards our understanding of biomolecular function. Calculating non-bonded forces (or in our case, electrostatic surface potential) is often a large portion of the computational complexity in analyzing biomolecular properties. Therefore, reducing the computational complexity of these force calculations, either by improving the computational algorithm or by improving the […]

May 5, 2011 by hgpu

Molecular mechanics simulations offer a computational approach to study the behavior of biomolecules at atomic detail, but such simulations are limited in size and timescale by the available computing resources. State-of-the-art graphics processing units (GPUs) can perform over 500 billion arithmetic operations per second, a tremendous computational resource that can now be utilized for general […]

October 30, 2010 by hgpu