GROMACS modification: No
I wonder whether the charged residues such as Lys, Arg, Asp, Glu and His residues, as well as the N and C termini are automatically set in charged state when using pdb2gmx command to transfer the pdb file to the gro file format. How could we check the charge state of these residues in a simulation system? How could we change the charge state of these residues? And how could I set the charge state of the system if I wish to simulation at specific pH?
Thank you in advance!