cumberworth / latticednaorigami_old Goto Github PK

For the current repository, please visit LatticeDNAOrigami.

Simulation package for lattice models of the self-assembly of DNA origami. The models are intended to include only the most important details for allowing an explicit representation of the geometry of the system. Simulations are run in the grand canonical ensemble, with annealing, Hamiltonian parallel tempering, and umbrella sampling variants available and configurable through a plain text input parameter file. Relatively general facilities are available for defining order parameters and associated bias functions in JSON formatted files. Output is in simple plain text file and JSON formats, and real-time visualization is possible with VMD via the bundled TCL scripts.

The core simulation package is implemented with C++14.

• boost
• JsonCpp
• openmpi (other backends may be used by the boost mpi wrapper)

Templates for running simulations and scripts for creating instances of input files can be found in scripts/simutils/. To see all configuration options, run

latticeDNAOrigami -h

To run a simulation, enter

latticeDNAOrigami -i [configuration file] > [log file]

To run a parallel simulation, enter

mpirun -np [procs] latticeDNAOrigami -i [configuration file] > [log file]

A python package for analyzing the results of simulations (origamipy) is also provided. Example scripts using the package are located in

scripts/analysis/

Analysis dependencies:

• python3
• python-numpy
• python-scipy
• python-matplotlib
• python-pymbar (for analysis of umbrella sampling simulations)

Configurations can be visualized in two ways. For vector based graphics, latex scripts using pgf/tikz library are provided in

scripts/tikz/

Alternatively, VMD may be used with the scripts provided in

scripts/vmd/