MacroDox Brownian Dynamics Software 
 
 

What is Brownian Dynamics?

Brownian dynamics (BD) is a powerful theoretical method to study intermolecular interactions in solution, such as diffusion controlled reactions, diffusional encounters. BD models the relative translation and rotational diffusive motion of whole macromolecules under the influence of complicated electrostatic and excluded volume interactions present in biophysical systems [1, 2].

BD simulations are carried out through the numerical integration of the Langevin Equation [3]. The Langevin dynamics incorporates stochastic terms, to describe the Brownian nature of the molecules in question. The Langevin equation incorporates two additional terms, namely:

1. A frictional or damping function that describes the frictional drag experienced by solutes in the cytosol or solutions with high effective viscosity.
2. A random force that is applied to mimic the random motion of both solvent and coincident solute particles.

The Brownian motion of interacting biomolecules in a solvent is simulated by a series of small displacements governed by the diffusion equations described by the Ermak and McCammon algorithm [1]. The particle displacement is computed from the Ermak-McCammon equation of translational and rotational motion, as implemented in the MacroDox program package.

1. Ermak, D. L.; McCammon, J. A., Brownian dynamics with hydrodynamic interactions. J Chem. Phys. 1978, 69 (4), 1352-1360.

2. Adcock, A. S.; McCammon, J. A. Molecular Dynamics: Survey of Methods for simulating the activity of proteins. Chem. Rev. 2006, 106, 1589 - 1615.

MacroDox Brownian Dynamics Software Features

1. Imports Protein Data Bank(PDB)-formatted protein coordinate files
2. Assigns masses and charges to every atom from a standard set of charges
3. Performs a Tanford-Kirkwood calculation to estimate the pKa's and mean charge on titratible amino acids
4. Assigns partial charges on residues based on Tanford-Kirkwood model
5. Computes various properties of the protein, such as solvent exposure of every atom, dipole moments, atom number density in concentric shells, estimated spherical radius, radius of gyration, translational diff coef, rotational diff coeff, and a list of atoms near the dipole vector ends
6. Computes electrostatic field grids around the protein based on iterative solutions of the linear and full Poisson-Boltzmann equation
7. Provides menus to set up and run Brownian Dynamics docking simulations on proteins. Either a full-blown atomic scale rough topology can be treated or the reaction between two spheres with embedded charges
8. A certain amount of analysis of complexes generated through Brownian Dynamics

MacroDox Brownian Dynamics Software Specifications

• Fortran90
• Compliled for Linux and UNIX systems
• Dynamic memory allocation recently added

Contact

Date: 08/21/06
Professor Kathryn A. Thomasson, Ph.D.
University of North Dakota
Chemistry Department
Abbott Hall Room 236
151 Cornell Street Stop 9024
Grand Forks, ND 58202-9024
email:kthomasson@chem.und.edu
last updated: 8/22/2006

MacroDox Authors

Dr. Scott H. Northrup, Dr. Katheryn A. Thomasson, George P. Stevenson, Theo L. Laughner, Andy Boswell, Kiran Mukhyala, Dr. Stephen L. Lowe, Dr. Victor F. Waingeh, Neville Forlemu

MacroDox is maintained by the research group of Kathryn A. Thomasson at the University of North Dakota

Professor Kathryn A. Thomasson, Ph.D.
Igor Ouporov, Ph.D.
Victor F. Waingeh, Ph.D.
Stephen L. Lowe, Ph.D.
Neville Forlemu