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