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

[zhmurov]

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

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