Using Anaconda or Miniconda to install SEEKR2 is recommended because their package and environment management capabilities ensure easy installation and compatibility. Users can either install from the conda-forge channel or manually install SEEKR2 from the source code, but the latter approach can be more time-consuming and error-prone. MD simulations in the SEEKR2 framework are run using the OpenMM or the Nanoscale Molecular Dynamics (NAMD) simulation engines. The OpenMM engine can be installed simultaneously during the conda installation of the SEEKR2 OpenMM plugin when users select to install the SEEKR2 package through conda-forge. OpenMM must be installed from source (See section 4.5.1) when users opt to install SEEKR2 from the source code. Alternatively, if OpenMM is not available or preferred, users can opt for the NAMD simulation engine. NAMD is a parallel MD code commonly accessible on computing clusters and supercomputers. It should be noted that although NAMD is a viable option for basic applications, not all SEEKR2 functionalities may be supported. Instructions for NAMD installation can be found at .