MDynaMix: a Molecular
Dynamics Program
Current
version: 5.3.0
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.
From version 5.3, all the further development of MDynaMix is transferred to Bitbucket repository:
MDynaMix at bitbucket
The code is freely distributed under
terms of GNU public
license
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