Applicability of Free Energy Calculations Using High–Throughput Grid Approach

Abstract

Free energy calculations tightly bind together experimental observations and computer-aided design through corresponding simulations at atomic level. Nowadays, free energy calculations represent a cornerstone for obtaining deeper insight into any biomolecular system, its molecular structure and especially dynamic behaviour. Despite this fact, several challenges have to be considered before routine utilization of this type of calculations. At first one has to deal properly with so-called sampling problem. Secondly, the appropriate way how to treat their extreme time demands has to be applied for obtaining converged and reliable data comparable with the experimental ones. Here we present the experience obtained through design, implementation and subsequent application of Multiple Walkers Approach (MWA) connected with Adaptive Biasing Force (ABF) and corresponding advantages and added values of MWA ABF run within distributed, heterogeneous grid environment under the EUAsia virtual organization (VO).