From your message, I assume that you want to exclude 1-5 and 1-6
pair interactions for specific pairs of atoms. I have not tried this,
but here are a few suggestions
1) Try using:
special_bonds lj 0 0 0 angle yes dihedral yes
If you want to turn off a particular 1-5 interaction, simply connect
them with a fake harmonic bond (with an infinitely weak spring, k=0).
Adding a bond between a pair of atoms will turn off the pair forces
between them (hopefully without effecting anything else).
Alternately, you can also do this with angles or dihedrals. For
example, you could use "special_bonds lj 0 0 0 angle yes" and
explicitly add an harmonic angle interaction between atoms 1,3,5.
This will switch off the interaction between that pair of atoms (1 and
5). Do this for all pairs of atoms whose interaction you wish to
switch off. (Just be sure to set the "k" for the angle force to
I think that this approach will work for you because molecules using
the TraPPE force-field have explicit angles and dihedrals between
every triplet (and quadruplet) of consecutively bonded atoms: 1,2,3
(or 1,2,3,4). This means that it will not effect your simulation if
you use "angle yes" "dihedral yes".
If I am wrong, then there are several other alternate ways to solve the problem:
2) Alternately you can try enabling all 1-2, 1-3, and 1-4 interactions using
special_bonds lj 1 1 1
Then you can manually control exactly which pairs of atoms are
interacting by explicitly connecting each pair of atoms you wish to
prevent from interacting with explicit bonds. Then use a careful
choice of parameters (or pair_style table) so that the bond-forces
exactly cancel out the (non-bonded) pair-forces interaction that would
otherwise exist between them:
Of course, you will want to delete those bonds when you try to
visualize the molecule.
3) If the methods above do not work, then a last resort, try this:
If your chains are short enough, you could define each of these atoms
with a unique type, and set the interaction between those types of
atoms to zero. (If you only want to do this for atoms in the same
chain molecule, but not different molecules, then you can try this
It suspect what you are trying to do should be possible in LAMMPS.
I hope this gives you some ideas.