Re-shape "small molecules" section: it shows how topologies work - Githubissues

zhmurov / mdcourse

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Re-shape "small molecules" section: it shows how topologies work #5

Open zhmurov opened 9 months ago

zhmurov commented 9 months ago

The idea of this section should be to show various aspects of GROMACS topology organization/files (.itp, rtp, via simulations of small molecules:

[x] .itp (Benzene)
[ ] .itp with parameters - (5CB)
[x] .rtp (Alkanes)
[ ] .hdb ??
[ ] special bonds to wrap molecule through PBC (silicone slab)