# MDynaMix: a Molecular Dynamics Program

## Version 5.0 from 20 Dec. 2006

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:

- NVT ensemble (v2.1)
- NPT ensemble (v3.0)
- complex DNA-like molecules (v3.5)
- non-cubic (rectangular) cell, optimized Evald sum calculation (v3.6)
- hydrogen bonds included (10-12 potential) (v3.7)
- first parallel version (v3.8)
- fully parallelized code (v4.0)
- several types of dihedral angles potentials, Morse bond potential (v.4.1) New (free) format of input data.
- option for separate pressure controll in each direction; reaction field method method for the electrostatic interactions; options for truncated octahedron or hexagonal simulation cell (v4.2)
- explicit reversible integrator for NPT-dynamics (Martyna et all, J.Chem.Phys, 101, 4177 (1994) is implemented; option for ASCII format of the restart file; some other options; more comments in the source files (v.4.3); utility "makemol" for easier constructing of molecular models is added
- v4.4 includes a large number of small changes, including possibility for separate Nose thermostats for each molecular species. Trajectory analysing utility (tranal) is also included into the package.
- v.5.0 reorganized input in the form "keyword value"; new documentation; new trajectory analysis suite

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:

- MDEE program - calculation of the free energy difference due to converting some of the molecules into non-interacting (ideal) particles using the expanded ensemble method. The molecular dynamics algorithm generally corresponds to MD v3.9
- TRANAL - additional analysis of trajectory files generated by the MD program.

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