MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by a force field consisting of Lennard-Jones, electrostatic, covalent bonds, angles and torsion angles potentials as well as of some optional terms, in a periodic rectangular, hexagonal or truncated octahedron cell.
Rigid bonds are constrained by the SHAKE algorithm. In case of flexible molecular models the double time step algorithm is used. Algorithms for NVE, NVT and NPT (including anizotropic NPT) statistical ensembles are implemented. Ewald summation is used for treatment of the electrostatic interactions. Computations of solvation free energies can be done by the expanded emsembles method with Wang-Landau optimization.
The program can be run both in sequential and parallel execution. The parallel version employs “replicated data” strategy. It can be run on any parallel architecture or workstation cluster with MPI parallel environment installed.
Utilities for preparation of molecular description files and for trajectory analysis are included.
The code is highly universal. It uses only standard Fortran statements and no external libraries (except MPI for parallel execution).
Website: www.fos.su.se/~sasha/mdynamix
Support: BitBucket Code Repository
Developer: Alexander Lyubartsev and Aatto Laaksonen
License: GNU General Public License
MDynaMix is written in Fortran. Learn Fortran with our recommended free books and free tutorials.
| Popular series | |
|---|---|
 | The largest compilation of the best free and open source software in the universe. Each article is supplied with a legendary ratings chart helping you to make informed decisions. |
 | Hundreds of in-depth reviews offering our unbiased and expert opinion on software. We offer helpful and impartial information. |
 | The Big List of Active Linux Distros is a large compilation of actively developed Linux distributions. |
 | Replace proprietary software with open source alternatives: Google, Microsoft, Apple, Adobe, IBM, Autodesk, Oracle, Atlassian, Corel, Cisco, Intuit, and SAS. |
 | Awesome Free Linux Games Tools showcases a series of tools that making gaming on Linux a more pleasurable experience. This is a new series. |
 | Machine Learning explores practical applications of machine learning and deep learning from a Linux perspective. We've written reviews of more than 40 self-hosted apps. All are free and open source. |
 | New to Linux? Read our Linux for Starters series. We start right at the basics and teach you everything you need to know to get started with Linux. |
 | Alternatives to popular CLI tools showcases essential tools that are modern replacements for core Linux utilities. |
 | Essential Linux system tools focuses on small, indispensable utilities, useful for system administrators as well as regular users. |
 | Linux utilities to maximise your productivity. Small, indispensable tools, useful for anyone running a Linux machine. |
 | Surveys popular streaming services from a Linux perspective: Amazon Music Unlimited, Myuzi, Spotify, Deezer, Tidal. |
 | Saving Money with Linux looks at how you can reduce your energy bills running Linux. |
 | Home computers became commonplace in the 1980s. Emulate home computers including the Commodore 64, Amiga, Atari ST, ZX81, Amstrad CPC, and ZX Spectrum. |
 | Now and Then examines how promising open source software fared over the years. It can be a bumpy ride. |
 | Linux at Home looks at a range of home activities where Linux can play its part, making the most of our time at home, keeping active and engaged. |
 | Linux Candy reveals the lighter side of Linux. Have some fun and escape from the daily drudgery. |
 | Getting Started with Docker helps you master Docker, a set of platform as a service products that delivers software in packages called containers. |
 | Best Free Android Apps. We showcase free Android apps that are definitely worth downloading. There's a strict eligibility criteria for inclusion in this series. |
 | These best free books accelerate your learning of every programming language. Learn a new language today! |
 | These free tutorials offer the perfect tonic to our free programming books series. |
 | Linux Around The World showcases usergroups that are relevant to Linux enthusiasts. Great ways to meet up with fellow enthusiasts. |
 | Stars and Stripes is an occasional series looking at the impact of Linux in the USA. |