GROMACS version:2023
GROMACS modification: Yes/No
Hello everyone,
I am new to gromacs and trying to generate a rmsd curve from gromacs for the Protein-ligand complex which could be similar to the schroedinger plot. But I am very comfused about how to choose group for the command gmx rms.
this is the reference picture from schoedinger sample, which is said the C-alpha curve is align on the Backbone, and lig fir prot is also align on Backbone. But when I choose Backbone for the second pick, C-alpha/UNL(ligand resname),my plot looks like a little strange
I am going to analysis if the ligand is proper for the protein, when the curve of ligand and protein varies almost the same, means that the ligand is relative stable in the protein.So anyone could tell me which pick order is right in this case?