MDynaMix (Molecular Dynamics of Mixtures) is a general-purpose molecular dynamics program for simulating mixtures of rigid and flexible molecules. It is designed for investigating molecular interactions and the thermodynamic behaviour of condensed-phase systems.
The program models molecules using force fields containing Lennard-Jones interactions, electrostatic forces and bonded potentials. It supports several periodic simulation cell geometries and can accommodate both constrained and flexible molecular structures.
MDynaMix provides statistical-mechanical simulation methods for studying systems under different thermodynamic conditions. Its capabilities include calculations of solvation free energies and methods for improving sampling of molecular configurations.
The software is written in Fortran and can operate sequentially or through parallel processing using MPI. It also includes utilities for preparing molecular descriptions and analysing simulation trajectories.
This is free and open source software.
Key Features
- Performs molecular dynamics simulations of mixtures containing rigid and flexible molecules.
- Supports Lennard-Jones, electrostatic, bond stretching, angle bending and torsional interaction potentials.
- Provides periodic simulation cells with rectangular, hexagonal and truncated octahedral geometries.
- Uses the SHAKE algorithm to constrain rigid molecular bonds.
- Supports multiple time-step integration for flexible molecular models.
- Offers simulations in microcanonical (NVE), canonical (NVT) and isothermal-isobaric (NPT) ensembles.
- Supports anisotropic pressure control for systems requiring independent cell dimensions.
- Includes Ewald summation for calculating long-range electrostatic interactions.
- Provides expanded-ensemble methods for calculating solvation free energies.
- Uses Wang-Landau optimisation to improve statistical sampling in free-energy calculations.
- Supports path integral molecular dynamics for incorporating quantum effects in atomic motion.
- Allows sequential simulations and parallel execution using MPI.
- Uses a replicated-data approach to distribute molecular dynamics calculations.
- Includes utilities for preparing molecular description files.
- Provides tools for analysing trajectories and calculating molecular properties.
Website: www.fos.su.se/~sasha/mdynamix
Support:
Developer: Alexander Lyubartsev and Aatto Laaksonen
License: GNU General Public License v2.0
MDynaMix is written in Fortran. Learn Fortran with our recommended free books and free tutorials.
Related Software
| Molecular Dynamics and Simulation Tools | |
|---|---|
| GROMACS | High-performance molecular dynamics simulations and analysis |
| LAMMPS | Classical molecular dynamics for materials and particle modelling |
| OpenMM | GPU-accelerated toolkit for custom molecular simulations |
| Orac | Parallel molecular dynamics for solvated biomolecular systems |
| MDynaMix | Molecular dynamics simulations of rigid and flexible mixtures |
| OpenMD | Molecular dynamics engine for complex materials and liquids |
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