I am quite new in the world of cloud computing that this might be an extremely silly question. I would like to run some GPU-simulations using the openmm environment. For that, I found that it is possible to install the required libraries as is google colab. See the code here:
print(sys.version) !wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh !bash Miniconda3-latest-Linux-x86_64.sh -bfp /usr/local !conda config --set always_yes yes !conda config --add channels omnia !conda config --add channels conda-forge !conda create -n openmm python=3.6 git rdkit openbabel openmm mdtraj nglview pymbar pdbfixer openmmforcefields openforcefields openmoltools parmed sys.path.append('/usr/local/envs/openmm/lib/python3.6/site-packages') # Of course I had to change this path to the appropiate one # install the openforcefield package directly from github. !pip install git+https://github.com/openforcefield/[email protected] import simtk.testInstallation simtk.testInstallation.main()
And then I need to run
!conda install ambertools
However, I have noticed that the libraries stay there only as far as the notebook is running. Thus, I was wondering if there is a method to create a notebook that already contains the libraries I need for the job from the start.
Thank you for your time.