change in environment files, input file, tutorial, init_notebooks
Changes
- init_notebooks to account for deprecation connected with IPython.display
- environment file change to have correct dependencies and to reduce deployment time on mybinder
- add an environment file without gromacs to use in specific case
- command line in the tutorial files to fix minor issue and to avoid dependence of MDanalysis from tpr file
- change em.mdp to make the non-bonded parameters consistent between em.mdp and df.mdp