Re: [Rdkit-discuss] Structure-Based Drug Design

2) For visualization nglview has lot of capabilities. I run simulation on a cluster and with nglview in a Notebook, the final trajectories can be directly be loaded in the notebook for visualization. Here is a gallery of different usages for visualization with

Re: [Rdkit-discuss] Structure-Based Drug Design

Dear James, Ad 1) Paolo Tosco did an integration of openMM and also was able to run a MD within Jupyter (partly covering (3)). Here is a link: https://github.com/rdkit/UGM_2017/blob/master/Presentations/Tosco_RDKit_OpenMM_integration.pdf Ad 2) About 5 years ago, James Davidson presented at the