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
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.