MDynaMix Source code

Latest stable version 5.2.7

md527.tar.gz ( 2015-01-31 )

Version history

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. The first parallel version was released in 1996 (v.3.8). Below is detailed list of changes after the program (v.4.1) was published in Computer Physics Communications, 128, 565-589 (2000).


- option for separate pressure control in each direction.

- reaction field method for treatment of electrostatic interactions

- improved memory-saving algorithm.

- cell of truncated octahedron and hexagonal geometry

Source code: md42.tar.gz


- subroutines were essentially regrouped into new files , more comments were inserted into the code.

- the MD algorithm for NVT or NPT ensemble was rewritten according to "modular-invariant" version of the Nose-Hoover thermostat, see G.J.Martyna, D.J.Tobais and M.L.Klein, J.Chem.Phys., v.101(5), p.4177 (1994)

- Cray - specific files added

- possibility to add any number of options in the input file

- Option "Cut large forces" properly implemented

- New "Makemol" utility

- Kong combination rule (J. Kong, J.Chem.Phys., 59, 2464 (1973)) for Lennard-Jones parameters for unlike atoms

Source code: md43.tar.gz

v. 4.4

- Option to read start configuration in "xmol" (xyz) format

- separate Nose thermostat for each molecular specii

- rewritten thermostat/barostat algorithm

- information on box sizes is included into commentary line of "xmol"-trajectory files

- tranal: can read trajectory in MDynaMix binary format, XMOL format and PDB format from GROMACS

- expanded ensemble version of the program (mdee) is updated and included into the package

Source code: md44.tar.gz

v. 5.0

- completely new input with keywords

- .mol files are now .mmol

- information on 1-4 scaling and some other features of force field is moved from main input to .mmol files

- option for "geometrical combination rule" for LJ sigma parameters

- new tranal package with modular structure

- new manual in latex-html format

Source code: md50.tar.gz

v. 5.1

- some internal reorganization of data structures

- path integral mode is implemented for NVT-ensemble simulations

- corrected anisotropic constant-pressure algorithm in the case of constraint dynamics

- option for separate barostat in XY-plane and Z-direction

Source code: md51.tar.gz


- Expanded ensemble mode with automatic tuning of parameters is implemented within the main MDynaMix code. The stand-alone mdee program is no longer supported

- Option of gradual change of volume ( Change_V slow) is added

- Option for semianizotropic NPT ensemble, with separate pressure ^M

control along Z-axis and in XY-plane, is introduced

Source code: md52.tar.gz

Improved Wang-Landau algorithm for optimization of expanded parameters

Source code: md524.tar.gz

Soft potentials in calculation of free energy by expanded ensemble

Source code: md525.tar.gz

Module cifo, converting crystallografic information in .cif format to MDynaMix .mmol and .smol molecular description formats, is added (contribution by Dmitrij Lioubartsev).

Possibility for special (not defined by the combination rules) parameters for Lennard-Jones cross-interactions

Source code: md526.tar.gz

Support for .mol2 files in building parameter-topology files

Source code: md527.tar.gz