Features of the previous version

From OxDNA
Revision as of 16:22, 16 April 2012 by Romano (talk | contribs)

Since oxDNA is still in its early stages of development, we release the code as-is with all the features enabled but we only give support to some of them. In particular, we provide examples and support to only molecular dynamics, Brownian dynamics and regular Monte Carlo simulations.

Supported features

Molecular and Brownian dynamics
The code can run both NVE and NVT simulations. The NVT ensemble can be enforced with two different kind of thermostats.
Regular Monte Carlo
regular Metropolis Monte Carlo simulations, with only nucleotide roto-translational moves, can be performed.
External forces
in order to favor motif formation or to mimic different environments, different kind of external forces can be applied to nucleotides or points in space. The complete list of available external forces can be found in the documentation.
A stand-alone single- and double-strand generator (UTILS/generate-sa.py)
An output-converter from oxDNA configuration files to .pdb and VMD-supported .xyz files (UTILS/traj2vis.py)

Unsupported features