BMOLogo
Publications

LMU München
Fakultät für Physik


Home

General
Research
Funding
Members
Publications
  All Publications
  PhD Theses
  Master Theses
  Search
  i Search
Lectures/Seminars
Conferences
Vacancies
Search

Internal




Impressum
(c) 2002 BMO

"Electrostatics of proteins in dielectric solvent continua. II. Hamiltonian reaction field dynamics."
Sebastian Bauer, Paul Tavan, and Gerald Mathias
J. Chem. Phys. 140, 104103 (2014)


Abstract:
In Part I of this work (J. Chem. Phys. 140, 104102, 2014) we have presented a reaction field (RF) method, which accurately solves the Poisson equation for proteins embedded in dielectric solvent continua at a computational effort comparable to that of polarizable molecular mechanics (MM) force fields. Building upon these results, here we suggest a method for linearly scaling Hamiltonian RF/MM molecular dynamics (MD) simulations, which we call "Hamiltonian dielectric solvent" (HADES). First, we derive analytical expressions for the RF forces acting on the solute atoms. These forces properly account for all those conditions, which have to be self-consistently fulfi lled by RF quantities introduced in Part I. Next we provide details on the implementation, i.e., we show how our RF approach is combined with a fast multipole method and how the self-consistency iterations are accelerated by the use of the so-called direct inversion in the iterative subspace. Finally we demonstrate that the method and its implementation enable Hamiltonian, i.e. energy and momentum conserving HADES-MD, and compare in a sample application on Ac-Ala-NHMe the HADES-MD free energy landscape at 300 K with that obtained in Part I by scanning of configurations and with one obtained from an explicit solvent simulation.

BMO authors (in alphabetic order):
Sebastian Bauer
Gerald Mathias
Paul Tavan

Assoziierte Projekte:
Long-range electrostatics in molecular dynamics simulations


WWW-Version

mailto: webmaster
Letzte Änderung: 2016-09-14 13:34