MDynaMix
Software for modelling molecules
From Wikipedia, the free encyclopedia
Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate mixtures of molecules, interacting by AMBER- and CHARMM-like force fields in periodic boundary conditions.[2][3] Algorithms are included for NVE, NVT, NPT, anisotropic NPT ensembles, and Ewald summation to treat electrostatic interactions. The code was written in a mix of Fortran 77 and 90 (with Message Passing Interface (MPI) for parallel execution). The package runs on Unix and Unix-like (Linux) workstations, clusters of workstations, and on Windows in sequential mode.
| Molecular Dynamics of Mixtures | |
|---|---|
DNA simulation on MDynaMix | |
| Original authors | Aatto Laaksonen, Alexander Lyubartsev |
| Developers | Stockholm University, Department of Materials and Environmental Chemistry, Division of Physical Chemistry |
| Initial release | 1993 |
| Stable release | 5.3.0
/ 15 January 2019[1] |
| Written in | Fortran 77-90 |
| Operating system | Unix, Unix-like, Linux, Windows |
| Platform | x86, x86-64, Cray |
| Available in | English |
| Type | Molecular dynamics |
| License | GPL |
| Website | www |
MDynaMix is developed at the Division of Physical Chemistry, Department of Materials and Environmental Chemistry, Stockholm University, Sweden. It is released as open-source software under a GNU General Public License (GPL).
Programs
- md is the main MDynaMix block
- makemol is a utility which provides help to create files describing molecular structure and the force field
- tranal is a suite of utilities to analyze trajectories
- mdee is a version of the program which implements expanded ensemble method to compute free energy and chemical potential (is not parallelized)
- mge provides a graphical user interface to construct molecular models and monitor dynamics process
Field of application
- Thermodynamic properties of liquids[4]
- Nucleic acid - ions interaction[5]
- Modeling of lipid bilayers[6]
- Polyelectrolytes[7]
- Ionic liquids[8][9]
- X-ray spectra of liquid water[10]
- Force Field development[11][12]