Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package.

ABSTRACT:

Background

Brownian Dynamics (BD) is a coarse-grained implicit-solvent simulation method that is routinely used to investigate binary protein association dynamics, but due to its efficiency in handling large simulation volumes and particle numbers it is well suited to also describe many-protein scenarios as they often occur in biological cells.

Results

Here we introduce our "brownmove" simulation package which was designed to handle many-particle problems with varying particle numbers and allows for a very flexible definition of rigid and flexible protein and polymer models. Both a Brownian and a Langevin dynamics (LD) propagation scheme can be used and hydrodynamic interactions are treated efficiently with our recently introduced TEA-HI ansatz [Geyer, Winter, JCP 130 (2009)

SUBMITTER: Geyer T 

PROVIDER: S-EPMC3098214 | biostudies-literature | 2011 Apr

REPOSITORIES: biostudies-literature