A new fast algorithm based on domain decomposition method for the computation of molecular dynamics in a polarizable, continuum solvent

  • Yvon Maday (Université Pierre et Marie Curie, Paris, France)
Felix-Klein-Hörsaal Universität Leipzig (Leipzig)


E. Cancès, L. Lagardere, F. Lipparini, Y. Maday, B. Mennucci, J.-P Piquemal, B. Stamm

In this contribution, we shall present an efficient, parallel, linear scaling implementation of the conductor-like screening model (COSMO), with van der Waals molecular cavities and classical charge distributions. The electrostatic energy contribution to the solvation energy, usually computed by solving an integral equation on the whole surface of the molecular cavity, can actually be computed by using an integral equation formulation of Schwarz’s domain decomposition method for boundary value problems.

We shall present in detail the implementation and its linear scaling properties, both in computational cost and memory requirements. Several numerical examples will also be presented on linear and globular large-sized systems, for which the calculation of the energy and of the forces is achieved with timings compatible with the use of polarizable continuum solvation for molecular dynamics simulations.

Cancès, E., Maday, Y., & Stamm, B. (2013). Domain decomposition for implicit solvation models. The Journal of chemical physics, 139, 054111.
Lipparini, F., Stamm, B., Cancès, E., Maday, Y., & Mennucci, B. (2013). Fast domain decomposition algorithm for continuum solvation models: Energy and first derivatives. Journal of Chemical Theory and Computation, 9(8), 3637-3648.

10/28/13 10/30/13

Numerical Analysis and Scientific Computing

Universität Leipzig Felix-Klein-Hörsaal

Katja Heid

Jörg Lehnert

Jürgen Jost

Max-Planck-Institut für Mathematik in den Naturwissenschaften

Felix Otto

Max-Planck-Institut für Mathematik in den Naturwissenschaften

Harry Yserentant

Technische Universität Berlin