Publications
FAMUSAMM: An Algorithm for Rapid Evaluation of Electrostatic Interactions in Molecular Dynamics Simulations
M. Eichinger H. Grubmüller, H. Heller and P. Tavan
Institut für Medizinische Optik, Theoretische Biophysik,
Ludwig-Maximilians-Universität München,
Theresienstr. 37, D-80333 München, Germany
J. Comput. Chem. 18: 1729- 1749, 1997
ABSTRACT: Within molecular dynamics simulations of protein-solvent systems the exact evaluation of long-range Coulomb interactions is computationally demanding and becomes prohibitive for large systems. Conventional truncation methods circumvent that computational problem, but are hampered by serious artifacts concerning structure and dynamics of the simulated systems. To avoid these artifacts we have developed an efficient and yet sufficiently accurate approximation scheme which combines the structure-adapted multipole method SAMM [C. Niedermeier and P. Tavan, J. Chem. Phys., 101, 734 (1994)] with a multiple-time-step method. The computational effort for MD simulations required within our fast multiple-time-step structure-adapted multipole method FAMUSAMM scales linearly with the number of particles. For a system with 36,000 atoms we achieve a computational speed-up by a factor of 60 as compared with the exact evaluation of the Coulomb forces. Extended test simulations show that the applied approximations do not seriously affect structural or dynamical properties of the simulated systems.
(C) 1997 John Wiley & Sons, Inc.
Keywords: molecular dynamics; protein dynamics; fast electrostatics computation; fast multipole method; multiple-time-step method