Features of the previous version

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 kinds 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 external environments, different kind of forces can be applied to nucleotides or points in space. The complete list of available external forces can be found in the documentation.

Stand-alone single- and double-strand generator

we provide a script (UTILS/generate-sa.py) which can be used to generate oxDNA input configurations with the command

generate-sa.py <box side> <file with sequence>

<box side> specifies the length of the box side in simulation units, while <file with sequence> must contain the sequence of the strands to be generated, one row per strand. If double strands are needed, each sequence must be preceded by DOUBLE:. A file with the layout

DOUBLE:AGGGCT

CCTGTA

would generate a double strand with a sequence AGGGCT and a single strand with a sequence CCTGTA.

Output-converter

we provide a script (UTILS/traj2vis.py) which converts oxDNA configuration files to .pdb and VMD-supported .xyz files. The usage is

traj2vis.py <pdb|xyz> <trajectory> <topology>

where the output format is either pdb or xyz, <trajectory> is the configuration (or whole trajectory) file and <topology> is the topology file. The output filename is <trajectory>.pdb or <trajectory>.xyz, depending on which output format has been chosen. If pdb is selected, then a commands.com file is generated, to be used with UCSF Chimera.

Unsupported features

The released version of oxDNA contains also code for

• MPI-powered parallel energy calculation
• Cluster-Move Monte Carlo (CMMC) simulations
• Forward Flux Sampling moleculary dynamics simulations
• Umbrella Sampling simulations
• Frenkel-Ladd CMMC free energy calculation
• A huge number of utility scripts which make working with strands easier. They are contained in the UTILS directory.