We present a set of tools that help in modelling biomolecular systems with coarse-grained molecular dynamics models: RedMDStream for model development and testing, and a simulation engine RedMD.

RedMDStream is a package for developing coarse-grained models for biomolecules (nucleic acids, proteins and their complexes) by automatizing and streamlining the most time consuming steps of the procedure. The software helps the researcher to efficiently design and tune such models (the representation, bonding patterns, potential energy function, force field parameters), either manually or by using an optimization algorithm. This software is designed for point-bead models, not bound to any lattice, with a small number of beads (1-4) representing one residue. RedMDStream uses RedMD as a simulation engine, the necessary source code is included in the RedMDStream bundle. The software is available for Linux under the GPL license.

RedMDStream Reference Manual is available here.

RedMDStream Quick Start tutorial is available here.

RedMDStream v. 1.0 sources are available here.

If you find RedMDStream useful please cite F. Leonarski and J. Trylska, RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models, Biophys. J., 108:1843-1847, 2015

 

RedMD is a an open source software to perform molecular dynamics simulations for coarse-grained models of proteins, nucleic acids and their complexes. Simulations can be carried out in the microcanonical ensemble, with Berendsen and Langevin thermostats, as well as with Brownian dynamics. We provide tools to generate initial configuration and topology from the PDB or PDB XML file formats. Force fields are based on the elastic network approach and its extensions. The code is written in C/C++ languages and the structure/topology of a molecule is based on an XML format.  The software is parallelized with OpenMP and MPI and available for Linux under the GPL license.

Manual (6.0MB) is available here.

RedMD sources are available here (November 13, 2013).

See Changelog for updates and bug fixes.

If you find our RedMD software useful please acknowledge its use by citing:

Adam Gorecki, Marcin Szypowski, Maciej Dlugosz, Joanna Trylska, RedMD - reduced molecular dynamics packageJ. Comput. Chem., 30:2364-2373, 2009

 

All questions and suggestions are welcomed at:

f.leonarski@cent.uw.edu.pl and joanna@cent.uw.edu.pl