RedMD (Reduced Molecular Dynamics)

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 OpenMP parallelized and available for Linux under the GPL license.

Manual (6.1MB) is available here. To download the software go to the registration page. See Changelog for updates and bug fixes. All questions and suggestions are welcomed at redmd@icm.edu.pl

Surface Diver

Mapping of physicochemical features onto surfaces of biomolecules can provide valuable insight into their function. Such information can be used to characterize and identify similarities in the surface regions of proteins. Surface Diver quantitatively describes various physicochemical properties such as hydrophobicity, charge density, and electrostatic potential of a biomolecule, using a method based on 3D Spherical Harmonic Decomposition. The method introduces a compact representation of a given property defined on the surface of the molecule using a finite set of rotation-invariant descriptors. Rotation-invariance of these descriptors allows one to compare proteins with respect to their shape and physicochemical properties without the need for any prior structural alignement. 

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