Paper Citing NAMD - Abstract
Cazade, P. -A.; Bordat, P.; Baraille, I.; Brown, R.; Smith, W.; Todorov, I. T.
DL_POLY_2 adaptations for solvation studies
MOLECULAR SIMULATION, 37:43-52, 2011
Adaptations of the molecular dynamics engine DL_POLY_2 were recently made to facilitate the investigation of questions arising mainly in the study of solvation dynamics. This paper presents the new facilities, with consideration of practical points for their efficient use and illustrative results obtained with them. Supplementary Information provides further details of their implementation to encourage future improvements and extensions. The adaptations of DL_POLY_2 for solvation studies are: Species by species and inter-species breakdown of the total energy for systems containing several species, such as solutions or models of adsorption, with, as an illustration, diffusion of a particular water molecule in a microporous silica zeolite, silicalite. The new facilities allow correlation of the trajectory of the molecule with its interaction with the host matrix. Solvation-induced spectral shifts, illustrated by the absorption shift and Stokes shift of a cyanoaromatic dye in solution in methanol. We discuss the relative importance of different contributions to the total spectral shift. Free energies by thermodynamic integration, illustrated by calculation of the excess free energy of liquid dimethylsulphoxide. We examine the use of different weighting functions for the mixed Hamiltonian to avoid or to delay divergence in thermodynamic integration.
