Summary
Brownmove is a simulation package for Brownian Dynamics (BD) and Langevin Dynamics (LD) simulations of many-particle systems, which handles variable numbers of rigid and bead-spring particles with electrostatic, van-der-Waals, and hydrodynamic interactions.
Researcher
Tihamér Geyer
Publication
Geyer, T. (2011) BMC Biophysics, vol. 4, no. 7, doi: 10.1186/2046-1682-4-7. Many-particle Brownian and Langevin dynamics simulations with the Brownmove package.
Description
“Brownmove” is a simulation package for Brownian Dynamics (BD) and Langevin Dynamics (LD) simulations of many-particle systems, which handles variable numbers of rigid and bead-spring particles with electrostatic, van-der-Waals, and hydrodynamic interactions. The particles, called proteins, are assembled hierarchically from one or more spherical shapes representing the different types of interactions. In addition to these moving proteins, the simulation box can be bounded with fixed walls of various types (reflecting, periodic, interfaces to reservoirs, or walls with physical interactions), which may also contain fixed structures. Protein and wall definitions can be set up at runtime from configuration files.
The BD and LD propagation algorithms are explained in U. Winter and T. Geyer, “Coarse Grained Simulations of a Small Peptide: Effects of Finite Damping and Hydrodynamic Interactions” (J. Chem. Phys. 131 (2009) 104103) and the algorithm for the fast hydrodynamics is published in T. Geyer and U. Winter, “An O(N2) approximation for hydrodynamic interactions in Brownian dynamics simulations” (J. Chem. Phys., 130 (2009) 114905). Some sample applications are described here.
Brownmove can be used as a black-box simulation tool or in your own projects as a library providing flexible particle and simulation setup, multiple types of interactions, Brownian and Langevin propagation algorithms, and basic output and analysis.
For a first impression, check out the ReadMe file, the documentation of the input file format, or the tutorials.
Download and Installation
Brownmove is distributed as source code. To compile and run it you need an ANSI C++ compiler and a recent version of the Gnu Scientific Library. Brownmove was developed, tested, and used on a variety of Linux and Mac OSX versions with g++ versions ranging from 2.95 to 4.6.
An archive with the latest source code (V 1.4, Sep. 25, 2012), documentation, and some tutorials can be downloaded here.
Bug fixes to the current version and older versions can be found here. Please note that g++ 4.6 throws a couple of warnings about obsoleted C format strings…
Licensing
The brownmove package is free for private or academic use. This means that the author retains the copyright, but you are free to use and modify the code for yourself or your non-commercial research projects. However, modifications must be clearly marked and documented and the reference to the original authors may not be deleted when you redistribute the code or parts thereof. The brownmove code comes with absolutely no warranty or liability, you are using it on your own risk.
If you want to use the code in a commercial product, please contact the author directly.