This repository is used to support the following work:
Yan Zhao, Shuting Cao, Yue Wang, Fan Li, Lixuan Lin, Linjie Guo, Fei Wang, Jie Chao, Xiaolei Zuo, Ying Zhu, Lihua Wang, Jiang Li* and Chunhai Fan*
It contains code for generating sequences of DFSM and example oxDNA files and Gromacs files for simulating DFSM from a DNA design tool and running equilibrium MD simulation. All the scripts and classes in this package can be used for other DNA framework projects. Please cite DNA framework state machine if you use this package for your work.
The shell scripts in this repository need to be run in a Linux environment.
Please use CUDA support to compile oxDNA and Gromacs to the path /opt.
All the files need to download and the shell scripts can be run directly in the Linux environment.
This folder contains examples of DNA-framework-state-machine for performing coarse-grained equilibrium simulations and all-atom molecular dynamics equilibrium simulations.
To run a simulation, please change the path to the directory containing the initial state and type:
./oxDNA_DNAmachine.sh
or
./GMX_DNAmachine.sh
All expected results can be reproduced. Simulations can be performed over days or weeks on a single Linux computer.