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Manuscript Title: ProtoMD: A Prototyping Toolkit for Multiscale Molecular Dynamics
Authors: Endre Somogyi, Andrew Abi Mansour, Peter J. Ortoleva
Program title: ProtoMD
Catalogue identifier: AEZN_v1_0
Distribution format: tar.gz
Journal reference: Comput. Phys. Commun. 202(2016)337
Programming language: Python 2.7.3.
Computer: x86 / x86 64.
Operating system: Linux.
RAM: Depends on the size of the system being simulated and duration of the simulation (few MBs to TBs)
Keywords: Python, Molecular dynamics, Multiscale, Coarse-graining.
Classification: 3, 4.12, 16.9, 23.

External routines: GROMACS (tested with versions 4.6x and 5.0x), MDAnalysis, GromacsWrapper, numpy, scipy, MPI

Nature of problem:
Prototyping multiscale coarse-grained algorithms for molecular dynamics.

Solution method:
Combining the open-source GROMACS molecular dynamics package and the python-based MDAnalysis library for running, debugging, and analyzing multiscale simulations

Restrictions:
The system under study must be characterized by a clear separation of timescales; otherwise, the multiscale algorithm fails to capture the slowly-varying modes.

Running time:
Depending on the problem size, simulations can take few hours to months.