MDynaMix: a Molecular Dynamics Program

Current version: 5.2.8

DNA animation This 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).

The basic principles behind the program are described in the following publication:

A.P.Lyubartsev, A.Laaksonen, MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures" Computer Physics Communications, 128, 565-589 (2000).

This is also the official reference. Please refer to us in any publication of the results obtained by this program.

Implementation of the expanded ensemble method for computation of solvation free energies is described in paper: J.P.M.Jämbeck, F.Mocci, A.P.Lyubartsev, A.Laaksonen, "Partial atomic charges and their impact on the free energy of solvation". Journal of Computational Chemistry, 34, 187-197 (2013).

Comments and bug reports are welcomed.

The code is freely distributed under terms of GNU public license