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# Introduction

MDynaMix is a general purpose molecular dynamics code for simulations of mixtures of rigid or flexible molecules, interacting by AMBER-like force field in a periodic cell. The program is well suited for simulations of flexible molecules based on the double time step algorithm. Alternatively, rigid bonds can be treated by the SHAKE algorithm. Algorithms for NVE, NVT and NPT ensembles are employed, as well as Ewald summation for treatment of the electrostatic interactions. The program can be run both in sequential and parallel execution, in the latter case the MPI parallel environment is required. The program is written in standard Fortran-77 and thus can be run on any computer system having a Fortran compiler.

The program is originally based on the MOLDYN program by Aatto Laaksonen, available from the CCP5 program library, Daresbury Lab, UK. Since 1993 many additional changes were made by Alexander Lyubartsev. The first parallelized version of the program (v.4.0) was published in:

A.P.Lyubartsev, A.Laaksonen, ``MDynaMix - a scalable portable parallel MD simulation package for arbitrary molecular mixtures" Computer Physics Communications, v.128(3), pp.565-589 (2000)

Please use this reference in any work made with the help of this package.

Apart the main MDynaMix block, the package includes the following components:

- makemol utility which provides some help in creation of files describing molecular structure and the force field
- tranal - a suite of utilities for analyzing trajectories
- mdee - a version of the program which implement expanded ensemble method for computation of free energy / chemical potential. MDEE program is not parallelized

Subsections

- Changes from previous versions

Next: Changes from previous versions Up: MDynaMix Package version 5.0 Previous: Contents