Programs in Physics & Physical Chemistry
|[Licence| Download | New Version Template] aeby_v1_0.tar.gz(270 Kbytes)|
|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.
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.
The test run provided takes approximately 6 minutes to run.
|Disclaimer | ScienceDirect | CPC Journal | CPC | QUB|