First of all, let me say that I am new to lammps. I will be conducting course grained simulations of protein fragments using a hybrid potential of charrm angles, charrm and helical dihedrals, LJ and Mercedes-Benz. One thing about my model is that the coefficients for the potentials vary based on each residues native secondary structure. (i.e. I need to specify, for each residue different coefficients).
The lammps documentation refers to specifying different coefficients for each potential type, but I am interpreting this as if the only one set of coefficients for dihedral type charrm and one for dihedral type helix not
Dihedral type charrm – alpha-helix: A = A1 d=d1
Dihedral type charrm - beta-sheet: A = A2 d=d2
Dihedral type charm – turn: A = A3 d = d3
Dihedral type helix – alpha-helix: A=A4 B=B1 C=C1
Dihedral type helix – beta-sheet: A=A5 B=B2 C=C2
Dihedral type helix – turn: A=A6 B=B3 C=C3
Some of the coefficients also depend on bead i-j pairings. Is there any way for me to specify the coefficients for each residue / residue pairing?