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Open Access Research article

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

Tihamér Geyer

Author Affiliations

Center for Bioinformatics, Saarland University, D-66123 Saarbrücken, Germany

BMC Biophysics 2011, 4:7  doi:10.1186/2046-1682-4-7

Published: 13 April 2011

Additional files

Additional file 1:

Brownmove definition file for a constrained bead-spring polymer. This (ASCII text) file defines a bead-spring polymer for a brownmove simulation with five beads connected by springs between the direct and the next neighbours. Each bead has a single van-der-Waals sphere to prevent mutual overlap between the beads, a sphere for hydrodynamic interactions, and two to four hook-up points for the connecting springs. For further details see the comments in this protein definition file.

Format: BDEF Size: 4KB Download file

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Additional file 2:

Simulation setup file for the bead-spring polymer examples. This (ASCII text) file defines the global parameters, which polymer to use, and the boundary conditions for the bead-spring polymer example simulations. For details see the comments in the file.

Format: BSC Size: 2KB Download file

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Additional file 3:

Example of a bead-train polymer definition file. This brownmove protein definition file gives an example for how a short bead-train polymer as sketched in Figure 2B can be defined in brownmove. It consists of three rotating beads which have a van-der-Waals sphere and off-center hooks for the springs between adjacent beads. For more details see the comments in the file.

Format: BDEF Size: 2KB Download file

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Additional file 4:

Brownmove definition file for the N = 13 "elastic protein". For more details see the comments in this (ASCII text) file.

Format: BDEF Size: 9KB Download file

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Additional file 5:

Simulation setup file for the diffusion-between-obstacles examples. Brownmove simulation setup file for a 2D periodic box with two oppositely placed constant density interfaces and an array of obstacles as sketched in Figure 9. The constant density interfaces and the obstacles are defined in "boxWithObstacles.bdef" which is given as additional file 6, while the mobile particles are defined in "simpleBead.bdef" (see additional file 7). For more details see the comments in the setup file.

Format: BSC Size: 3KB Download file

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Additional file 6:

Brownmove definition file for a simulation box with two constant density interfaces and a central array of fixed spherical obstacles (see Figure 9). For more details see the comments in this (ASCII text) file.

Format: BDEF Size: 4KB Download file

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Additional file 7:

Brownmove particle definition file for a minimal spherical, uncharged, van-der-Waals particle used in the diffusion-between-obstacles example.

Format: BDEF Size: 1KB Download file

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Additional file 8:

Brownmove particle definition file for the agglomeration-with-network-analysis example simulation. As sketched in Figure 10 A the particle consists of two displaced van-der-Waals spheres with different "colour" indices. Together with the parameter definitions in the simulation setup file (see additional file 9) the spheres with colour 0 can stick to each other while all other pairs have purely repulsive interactions. For more details see the comments in this (ASCII text) file.

Format: BDEF Size: 1KB Download file

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Additional file 9:

Brownmove simulation setup file for the agglomeration-with-network-analysis example simulation.

Format: BSC Size: 3KB Download file

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