Dear lammps users,
I am studying a protein adsorption. In articles there are some reports like alfa helix and residue number percent and so on… can I extract these with Lammps? Can I also calculate the kind and amount of different bonds in out put? I just calculated the radius of gyration and potential energy but I need more items for describing the protein changes. Could you please help me about this? How can I study the protein properties more by lammps?
Best regards,
Runak
What features are available in LAMMPS are documented in the LAMMPS manual. No functionality gets added without being documented. Therefore, if it is not in the manual, LAMMPS cannot do it (or it won’t work).
But that doesn’t mean you cannot compute those properties, you just need to use some other tool. Please see here: https://www.lammps.org/prepost.html and here: https://www.lammps.org/viz.html
Please note that LAMMPS trajectories do not contain information about residues and other protein specific properties, so you may have to build or revert to corresponding topology files (e.g. a .psf file) that do.
Axel.