MDynaMix

File:MDynaMix-MGE.png

DNA simulation on MDynaMix

MDynaMix (an acronym for Molecular Dynamics of Mixtures) is a general purpose molecular dynamics software package for simulations mixtures of molecules, interacting by AMBER/CHARMM like force fields in a periodic boundary conditions. MDynaMix is developed at the Stockholm University, Sweden. Algorithms for NVE, NVT, NPT and anisotropic NPT ensembles are employed, as well as Ewald summation for treatment of the electrostatic interactions. The code was written in Fortran 77 (with MPI for parallel execution) and C++ and released under the GNU GPL. The package works on Unix/Linux workstations and clusters of workstations as well as on Windows in sequential mode.

Programs

• md - the main MDynaMix block
• makemol is a utility which provides help in creation of files describing molecular structure and the force field
• tranal is a suite of utilities for analyzing trajectories
• mdee is a version of the program which implement expanded ensemble method for computation of free energy/ chemical potential (is not parallelized)
• mge provides graphical interface for molecular models construction and monitoring of dynamics process

Field of application

• Thermodynamic properties of liquids
• Nucleic acid - ions interaction
• Modeling of lipid bilayers
• Polyelectrolytes
• Ionic liquids
• X-ray spectra of liquid water
• Force Field development

See also

2

External links

• Home page
• Ascalaph, graphical shell for MDynaMix (GNU GPL)