# MDynaMix: a Molecular Dynamics
Program

## Current version: 5.2.7

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 statistical ensembles are
implemented, as well as Ewald sum for treatment of the electrostatic
interactions. Treatment of quantum correction to the atomic motion
can be done within the Path Integral Molecular Dynamics approach.
Possibility for free energy computations by the expanded ensemble
method with Wang-Landau optimization of the balancing facor is included
from v.5.2.

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. Trajectory analysis suite is
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

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