Comments L4

[raquellrios]

Comments:

• On slide 8 in "Solvate in water and add ions", I would add that the system is (normally) neutralised.
• On slide 11 I would add a short sentence about why PBC are needed (e.g. reduce finite size effects). Additionally, on this slide I would also add a Why? question to semi-isotropic pressure coupling in membranes so that students are encouraged to think about why this might be.
• (Optional) On slide 12 add that these timesteps values are for all atomistic simulations.

[raquellrios]

Comments on P4:

• The first step of this practical is the topology. However the concept of topology is not really introduced in L4. Therefore, I believe an explanation of topology should be included in the tutorial (or lecture). It is a very key concept of MD simulations so I think it should be briefly explained in one of the two.
• As mentioned by the other reviewer, only lig27_smiles = "[H:7][C@:6]1([C:13](=[C:11]([C:9](=[O:10])[O:8]1)[O:12][H:19])[O:14][H:20])[C@:3]([H:4])([C:2]([H:16])([H:17])[O:1][H:15])[O:5][H:18]" works
• When TIP3P is mentioned after cell 11, I would just add that this is a three point charge water model.