Molecular: Novel approaches for the evaluation of long range electrostatic interactions in MD

The calculation of electrostatic interactions in molecular computer simulations is by far most time-consuming part due to their long-ranged nature. In the last few years some promising algorithm to treat long range interactions based on Non Uniform FFT has been proposed. The use of non uniform sampling grids could considerably speed up this performance, allowing us to simulate more realistic (large number of atoms) systems. We implemented a novel O(N log N) approach, that combines the traditional Ewald summation technique with the nonuniform Fast Fourier transform to calculate the electrostatic energies and forces in molecular computer simulations.

The context of the project is an MD code named MDynaMix [1]. It is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field in a periodic cell. MDynaMix is a diffused MD tools, widely used since the early 90’s for the study of several inorganic and biological systems. The goal of this project is to perform a major evolution of MDynaMix code, allowing it be up to date respect the new hardware and algorithmic releases that are now coming out, implementing a novel approach by combining the traditional Ewald summation technique – which, either as exact or in some approximate scheme, is usually employed in the simulation of the nucleic acids – with the non-uniform Fast Fourier transform. This method (ENUF [2]) is both highly efficient, scaling as (N log N) and straight-forward to implement in existing simulation programs; implementation will based on utilize of widely available libraries.