MD post processing analysis

[lauraf244]

Hello,
can anyone help me with the best script to do the following analysis with mda on a xtc trajectory obtained with LAMMPS:
1)Calculation of interaction energy (for example among one substrate and the solvent in the MD simulation)
2)Number of H bonds (for example among the two type of molecules of a solvent)
3) Distribution of the torsional angle of the substrate

Thank you much for your help

[orbeckst]

1. MDAnalysis does not calculate energies. You need to use your MD engine for that.
2. H-bonds: see User Guide: Hydrogen Bond Analysis with the tools in MDAnalysis.analysis.hydrogenbonds
3. Substrate torsions: select the substrate, then define the torsions of interest as atomgroups (make sure that the order is correct, e.g.. by doing an ordered selection or slicing the atomgroup with indices (eg ag = u.atoms[[0, 1, 10, 9]]), and then use ag.dihedral.value() to get the value. A while back I tried to automate dihedral finding in small molecules with the SMARTS='[!#1]~[!$(*#*)&!D1]-!@[!$(*#*)&!D1]~[!#1]' and you're welcome to look at the code in molconfgen.chem, perhaps it's useful. You should learn using RDKit for this kind of stuff (see also MDAnalysis blog post on the RDKit converter in MDAnalysis from 2020).