Hey there people! I am currently learning GROMACS and trying to perform a protein-ligand interaction simulation. The tutorials I follow suggest using CHARMM36 and it seems fit because it is an all-atom force field. But the structure I am working on is a protein-DNA complex and the binding residue also contains nucleic acid residues. When I am preparing the protein-DNA complex topology with pdb2…

As part of an assigment I was required to calculate in ORCA the first 4 excited states of pyridine using the 6-31G* basis set, once with the CIS(D) method and once with TD-DFT using the B3LYP functional. Here is a summary of what I got. But the order of excited states is quite different when comparing the methods, and I was asked to give some sort of explanation ofr this, and I really got not…