Open Source C++ Molecular Mechanics Software

This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/

We are proud to introduce version 5 of CAMPARI. We have added a number of new features, most notably a Python interface for interpreting user-supplied code (with the help of ForPy), a novel trajectory storage standard (with the help of libpqxx/PostgreSQL), and a module for performing transition path theory. Naturally, CAMPARI continues to provide the reference implementation of the ABSINTH force field paradigm and implicit solvation model. CAMPARI is a joint package for performing and analyzing molecular simulations, in particular of systems of biological relevance. It focuses on a wide availability of algorithms for (advanced) sampling and is capable of combining Monte Carlo and molecular dynamics in seamless fashion. CAMPARI offers the user a very high level of control over all implemented features. For more information and features, please refer to the project's homepage at http://campari.sourceforge.net/V5

rDock is a fast and versatile Open Source docking program that can be used to dock small molecules against proteins and nucleic acids. It is designed for High Throughput Virtual Screening (HTVS) campaigns and Binding Mode prediction studies. rDock is mainly written in C++ and accessory scripts and programs are written in C++, perl or python languages. The full rDock software package requires less than 50 MB of hard disk space and it is compilable in all Linux computers. Thanks to its design and implementation, it can be installed on a computation cluster and deployed on an unlimited number of CPUs, allowing HTVS campaigns to be carried out in a matter of days. The rDock program was developed from 1998 to 2006 by the software team at RiboTargets (subsequently Vernalis (R&D) Ltd). In 2006, the software was licensed to the University of York for maintenance and distribution. In 2012, Vernalis and the University of York agreed to release the program as Open Source software.

Molecular Graphics, Molecular Dynamics, Optimization, Quantum chemistry. Molecular model building. Explicit and implicit water models. http://www.biomolecular-modeling.com/Products.html

APL@Voro is a program designed to aid in the analysis of lipid bilayer simulations carried out by gromacs. It calculates the area per lipid and the membrane thickness even for mixed bilayers. Colored Voronoi diagrams and different types of plots are presented in an interactive environment.

QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.

ESTReMo is a genetic algorithm-based simulator to explore the evolution of transcription factors and their binding motifs on realistic genomic backgrounds.

The OFR method is a type of steered molecular dynamics method for determining potentials of mean force (PMF) (Phys. Rev. E, 2011, 83: 021114) and local diffusion coefficients, D(z) (Phys. Rev. E, 2012, 86: 036707). OFR-AT is a fast and convenient program for analyzing large output data files from the OFR method, and returns the information necessary to quickly and easily calculate the PMF and D(z) in a spreadsheet. The software is described in detail in the following article: J. Comp. Phys., 231(11): 4355-4364.

An open-source software aimed at computing cavity accessibility in cyclodextrin derivatives

This is a general open source Quantum Mechanics/Molecular Mechanics project with academic origin. Its intention is to produce free software tools to study molecular systems through QM/MM, in open collaboration.

Visualization of TASEP, ASEP, SSEP models with various update rules based on Zarja simulation library using QT GUI library.

This is bionically project.

chemkit is an open source software library for chemistry applications, particularly in the areas of cheminformatics, molecular visualization and molecular modeling.

ParticleVis is a visualization tool specialized for loading and exploring particulate simulation data. It contains a set of features that enables powerful and useful visualizations of particle simulations to be quickly generated. Support is provided for visualization of hundreds of thousands of particles on commodity workstations, using OpenGL. Functionality includes data exploration, debugging of simulation output, and generation of presentation-quality imagery. The ability to visualize vector flow information in a variety of forms, such as arrow-lines, inscribed glyphs, and motion blurred particles, is particularly useful in the study of granular flows. User-generated information can be integrated into the visualization using features such as per-particle color maps and surface maps, per-region vector fields, and volumetric data.