Running the Code

Requirements

In order to run DNAfold, your must have the following installed on your system:

  • Git

  • GNU Make

  • C++ Compiler

Furthermore, we recommend running the code on WSL, MacOS, or a Linux OS (we have tested Ubuntu and CentOS).

Cloning

The DNAfold code is hosted on GitHub. Before cloning, enter the folder in which you want to store the code.

mkdir <MYCLONE>
cd <MYCLONE>

Then clone the repository.

git clone https://github.com/marcello-deluca/dnafold

This creates a folder called dnafold/ which contains two relevant folders:

  • src/ contains the source simuation code.

  • examples/ contains several example structures with corresponding input files.

To create the executable required to run the code, run the following commands:

cd src
make clean
make

This creates an executable called dnafold in the root directory. The code is now ready to run.

Running

First, create and enter a folder in which you want to store all the input and output files for your simulation.

mkdir <MYSIM>
cd <MYSIM>

Add the caDNAno design (see caDNAno Examples) and the parameters file (see Parameter Descriptions) to the folder. Make sure the parameters file correctly references the name of your caDNAno design.

Finally, run the following command to begin the simulation, making sure to substitute <PATH_TO_DNAFOLD> with the path to the dnafold executable created earlier.

<PATH_TO_DNAFOLD>/dnafold input.txt

To run the program in the background and save the standard output to a file, use the following command:

nohup <PATH_TO_DNAFOLD>/dnafold input.txt >> report.out 2>&1 &

The simulation should then begin!

Visualization

We recommend using OVITO to visualize the simulation results.