# CHARMM LJ Parameters

Hello All,

I’m am using the CHARMM22 parameter set with pair style lj/charmm/coul/long. CHARMM22 defines the nonbonded parameters with:

NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -
cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5
!adm jr., 5/08/91, suggested cutoff scheme
!
!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
!
!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
!
!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4
!
!carbons
C 0.000000 -0.110000 2.000000 ! ALLOW PEP POL ARO
! NMA pure solvent, adm jr., 3/3/93
CA 0.000000 -0.070000 1.992400 ! ALLOW ARO
! benzene (JES)
CC 0.000000 -0.070000 2.000000 ! ALLOW PEP POL ARO

The one thing I noticed was the Rmin is given as “Rmin/2” and in the LAMMPS section for the CHARMM LJ there is this note:

“Note that sigma is defined in the LJ formula as the zero-crossing distance for the potential, not as the energy minimum at 2^(1/6) sigma.”

So, am I correct in needing to multiply the given Rmin by 2/(2^(1/6)) in order to have the proper conversion while only taking the absolute value of epsilon?

Joe

That's really a Q about how CHARMM22 defines its sigma.
If it is different than the formula listed on the LAMMPS doc
page for that pair style, then you do indeed need to scale it.

For a complex system, I suggest you run it (even for 0 steps)
in another code (e.g. CHARMm) and compare the energies
and forces (pressure) against LAMMPS, which will give
you confidence you have set everything up correctly.

Steve

Unfortunately I don’t have access to CHARMM (It’s why I’m using the freely available LAMMPS code and CHARMM parameter set).

Unfortunately I don't have access to CHARMM (It's why I'm using the freely
available LAMMPS code and CHARMM parameter set).

you can compare to NAMD for example.

axel.