Page History

...

1. Activate the openmm environment using the following command:
   
   source activate openmm
   
   

2. Configure the Anaconda package manager to include the omnia and conda-forge channels. This will allow you to access the necessary dependencies from these channels. To do this, run the following commands in a terminal:

   conda config --append channels omnia
   conda config --append channels conda-forge

    

3. Install open3SPN2 using the Anaconda package manager. To do this, run the following command in a terminal:

   conda install -c wolynes-lab open3spn2

    

4. Install X3DNA >= 2.4. This is necessary for open3SPN2 to run properly. To do this, follow the instructions on the X3DNA website: http://x3dna.org/

    

5. Set the X3DNA environment variable to the location of the X3DNA installation folder. This will allow open3SPN2 to find the X3DNA executables. To do this, run the following command in a terminal, replacing /path/to/x3dna-v2.4 with the actual path to the X3DNA installation folder:
   
   export X3DNA=/path/to/x3dna-v2.4
   
   
6. If you want to use open3SPN2 for protein-DNA simulations, you will also need to install openAWSEM. To do this, you must have followed the previous instruction. Also add the openAWSEM path to the PYTHONPATH environment variable. This will allow open3SPN2 to import openAWSEM modules. To do this, run the following command in a terminal, replacing /path/to/openawsem with the actual path to the openAWSEM installation folder:
   
   export PYTHONPATH=/path/to/openawsem:$PYTHONPATH
   
   
7. If you want to install open3SPN2 locally instead of using the Anaconda package manager, you can clone the open3SPN2 repository from GitHub and install it manually. To do this, run the following commands in a terminal:
   
   git clone https://github.com/cabb99/open3spn2.git
   cd open3spn2
   pip install -e .
   
   
8. After completing these steps, you should be able to use open3SPN2 on your computer. Keep in mind that you will need to set the X3DNA and PYTHONPATH environment variables every time you open a new terminal or log in to your computer. If you want these variables to be set automatically, you can add the export commands to your .bashrc file. This will set the environment variables every time you open a new terminal.

...