MDynaMix: a Molecular Dynamics Program

Version 5.0 from 20 Dec. 2006

DNA animation This is a general purpose molecular dynamics code for simulations of mixtures of either rigid or flexible molecules, interacting by AMBER- or CHARMM-like force field in a periodic rectangular cell. In the case of flexible molecules the double time step algorithm is used. Algorithms for NVE, NVT and NPT statistical ensembles are employed, as well as optimized Ewald sum for treatment of the electrostatic interactions. The program can be run both in sequential and parallel execution. The parallel version employes "replicated data" strategy. It can be run on any parallel architecture or workstation cluster with MPI parallel environment installed.

This program was 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, some of these are:


RAM Memory: depends on the simulated system and on which data you want to get from the simulations. 256Mb is enough in most of simulations involving up to 20000 atoms. The program was tested even for simulations of 50000 atoms (see example)

The code is highly universal. It uses only standard Fortran-77 statements and no external libraries (except MPI for parallel execution). There should be no problem to compile the code on other architectures.

Some results on MD simulation of DNA in presence of water, Na+ and Cl- ions, are available

Related software:

A detailed description of the parallel agorithm is available here (pdf file). 

The current version of the program (Fortran-77) may be downloaded from md50.tar.gz (3.3M). Previous version 4.4 is also available: md44.tar.gz. Please reffer to us in any publication of the results obtained by this program. The relevant reference (which is also a manual) is: A.P.Lyubartsev, A.Laaksonen, MDynaMix - A scalable portable parallel MD simulation package for arbitrary molecular mixtures" Computer Physics Communications, 128, 565-589 (2000).

On-line manual is available

Comments and bug reports are welcomed.


Alexander Lyubartsev