Setting potential coefficients on a per-bead basis

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1

Hello Everyone,

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?

TIA,

Rob

2

Hello Everyone,

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

That is not correct.

3

to be more explicit.

each dihedral (or bond, angle etc.) is assigned a type number and then
for each type number, you can assign a set of coefficients (and in the
case of hybrid styles also a style). you can have as many type numbers
as you want (well, up to about 2 billion IIRC).

4

Oh that's great, that allows me to get up and running much faster.

Thanks Axel!

Rob