gmx solvate places waters inside the protein

[pbuslaev]

The problem is that gmx solvate can put waters inside the hydrophobic environment. There are multiple ways to overcome the issue. One would be to get read of all waters that have fewer than a certain number of neighbouring waters

[i-Molecule]

packmol can be useful for this task

[pbuslaev]

packmol uses tcl. Not sure that we can easily run it on Google Colab/Jupyter. But we can check the algorithms and implement them in python