Development of an Advanced Implicit Solvent Model in DL_POLY

A library, implementing the AGBNP2 [1, 2] implicit solvent model that was developed within PRACE-2IP [3] is integrated into the DL_POLY_4 [4] molecular dynamics package in order to speed up the time to solution for protein solvation processes. Generally, implicit solvent models lighten the computational loads by reducing the degrees of freedom of the model, removing those of the solvent and thus only concentrating on the protein dynamics that is facilitated by the absence of friction with solvent molecules. Furthermore, periodic boundary conditions are no longer formally required, since long-range electrostatic calculations cannot be applied to systems with variable dielectric permittivity. The AGBNP2 implicit solvation model improves the conformational sampling of the protein dynamics by including the influence of solvent accessible surface and water-protein hydrogen bonding effects as interactive force corrections to the atoms of protein surface. This requires the development of suitable bookkeeping data structures, in accordance with the domain decomposition framework of DL_POLY, with dynamically adjustable inter-connectivity to describe the protein surface. The work also requires the use of advanced b-tree search libraries as part of the AGBNP library, in order to reduce the memory and compute requirements, and the automatic derivation of the van der Waals radii of atoms from the self-interaction potentials.