Paper Citing NAMD - Abstract
Bauer, Sebastian; Tavan, Paul; Mathias, Gerald
Exploring Hamiltonian dielectric solvent molecular dynamics
CHEMICAL PHYSICS LETTERS, 612:20-24, SEP 18 2014
Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an a-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation. (C) 2014 Elsevier B.V. All rights reserved.
