Molecular Dynamics

The EJS Molecular Dynamics model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated time step. For sufficiently small time steps dt,...

The EJS Molecular Dynamics Demonstration model is constructed using the Lennard-Jones potential truncated at a distance of 3 molecular diameters. The motion of the molecules is governed by Newton's laws, approximated using the Verlet algorithm with the indicated Time step. For sufficiently small...

The Molecular Dynamics Adiabatic Piston model shows two gas samples within a horizontal cylinder that is divided by an insulated piston that moves without friction. It is a supplemental simulation for an article by Eric Gislason "A close examination of the motion of an adiabatic piston" in the...


Platforms: Mac

PFMD performs a Molecular Dynamics simulation of some polarizable fluids at the liquid state by means of a dissociable potential. Supported molecules are H2O (water) and MX3, where M is a metal among Al, Fe, or Ga and X is a halogen among Cl, Br, or I.


Platforms: Windows, Mac, Linux

LAMMPS project is a Molecular Dynamics Simulator. LAMMPS has potentials for soft materials (biomolecules, polymers) and solid-state materials (metals, semiconductors) and coarse-grain systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the mesoscale...


Platforms: *nix

Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Windows

Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Mac

Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Windows

Open3DALIGN is an open-source software aimed at unsupervised molecular alignment. Open3DALIGN is a command-line tool which is operated by means of a few commands which can be entered interactively from a command prompt, read from a batch script or piped through standard input. If PyMOL is...


Platforms: Linux

GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins, lipids and nucleic acids that have a lot of complicated bonded...


Platforms: Mac, Linux

jSim for Gromacs is a Graphical User Interface for the Molecular Dynamics Package Gromacs. It has a project style interface to organize your md simulations. It is also possible to start md simulations on remote computers with ssh.


Platforms: Windows, Mac, Linux

This project aims to develop a cross platform environment for utilisation of various open source and freely available molecular dynamics and bioinformatics tools. Some extra features are included such as protein hydrophobicity and hydrophilicity plots.


Platforms: Windows, Mac, Linux

MDAnalysis is an object-oriented python toolkit to analyze molecular dynamics trajectories generated by CHARMM, Gromacs, NAMD, LAMMPS, or Amber. It allows one to read molecular dynamics trajectories and access the atomic coordinates through numpy arrays. This provides a flexible and relatively...


Platforms: Mac

Ascalaph Graphics is a program for molecular graphics and dynamics, as well as a graphical shell to package of molecular dynamics MDynaMix. Features: Molecular graphics Multiple windows Two cameras per model CPK, Wire frame, Stick, Ball and Stick and CPK Wire frame styles Molecular...


Platforms: *nix

The Ascalaph Designer application was developed for molecular models and simulations. Using this application you can simulate, molecular graphics, optimization, molecular dynamics, quantum chemistry. Features: Molecular graphics Multiple windows Two cameras per model CPK, Wire frame,...


Platforms: Windows

MDDriver is a library allowing a user to easily couple molecular visualisation tools with simulation code through a network. It allows to carry out interactive molecular dynamics, visualize simulation results and drive a simulation in interactive time.


Platforms: *nix

gOpenMol is a tool for the visualization and analysis of molecular structures and their chemical properties. The program uses Tcl/Tk scripting engine and can thus be easily extended without modifying the kernel code. gOpenMol can also be extended by writing extensions using sharable objects...


Platforms: *nix

ToBiX is a Morphix-based Linux live CD containing a range of specialist applications for bioinformatics. With this distrubution you just boot from the CD and you have a fully functional LINUX OS distribution with open source applications. Besides using some RAM, ToBiX doesnt touch the host...


Platforms: *nix

APBS was designed as a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation or PBE. PBE is one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. Continuum...


Platforms: Windows

Pizza.py is a collection of Python tools that perform pre- and post-processing for the LAMMPS molecular dynamics package (or other simulators). Software wrapped by Pizza.py, so it can be invoked from Python, includes GnuPlot, MatLab, Raster3d, and RasMol


Platforms: Mac, Linux