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Manuscript Title: MDVRY: a polarizable classical molecular dynamics package for biomolecules
Authors: M. Souaille, H. Loirat, D. Borgis, M.P. Gaigeot
Program title: MDVRY
Catalogue identifier: AEBY_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 180(2009)276
Programming language: C.
Computer: Linux machines with FFTW Fourier Transform package installed.
Operating system: Linux machines, SUSE & RedHat distributions.
Keywords: Molecular dynamics, Electrostatics, Polarization, Induced point dipoles, Thole, Car-Parrinello type of dynamics, Biomolecules.
PACS: 61.20.Ja, 61.25.Em.
Classification: 3, 16.13, 23.

External routines: FFTW, (http://www.fftw.org/)

Nature of problem:
Molecular Dynamics Software package.

Solution method:
Velocity Verlet algorithm. The implemented force field is composed of intra-molecular interactions and inter-molecular interactions (electrostatics, polarization, van der Waals). Polarization is accounted through induced point dipoles at each atomic site. Supplementary degrees of freedom are associated to the induced dipoles so that a modified Hamiltonian of the dynamics is written. This allows to calculate the induced dipoles with a very fast 'Car-Parrinello' type of dynamics.

Running time:
The test run provided takes approximately 6 minutes to run.