Small doubt regarding special_bond fene

Dear Axel,

I am sorry, still a bit of confusion. I shall try to explain my confusion in four steps. Please let me know where is the flaw?

1)LAMMPS manual says that “For purposes of computing weighted pairwise interactions, 1-3 and 1-4 interactions are not defined from the list of angles or dihedrals used by the simulation. Rather, they are inferred topologically from the set of bonds specified when the simulation is defined from a data or restart file (see read_data or read_restart commands)”. So if I have a moleucule 1 connected to 2 and 2 connected to 3, LAMMPS automatically takes the distance between 1 and 3 as 2 bonds from topology, isnt it?

  1. If step 1 is correct, the special_bonds command: “special_bonds fene” (default 0 1 1) will calculate the repulsive LJ interaction included in FENE potential between 1 and 3 at full strength as lammps knows what molecule is 2 bonds away from topology.

  2. Then if I include a lj/cut to this, then the net potential will count LJ interactions twice (one from FENE and other from lj/cut) between molecule 1 and 3.

  3. If till Step 3 is correct, then it becomes like interactions between molecule 1 and 3 or molecule 1 and 4 will have contributions from two LJ terms (FENE and lj/cut) where as interactions between 1 and any other molecule (5 to N) will have only one LJ term (that is from lj/cut).

Am I making some fundamentally wrong assumption?

Thanks in advance

Regards

Dear Axel,

I am sorry, still a bit of confusion. I shall try to explain my confusion in
four steps. Please let me know where is the flaw?

1)LAMMPS manual says that "For purposes of computing weighted pairwise
interactions, 1-3 and 1-4 interactions are not defined from the list of
angles or dihedrals used by the simulation. Rather, they are inferred
topologically from the set of bonds specified when the simulation is defined
from a data or restart file (see read_data or read_restart commands)". So if
I have a moleucule 1 connected to 2 and 2 connected to 3, LAMMPS
automatically takes the distance between 1 and 3 as 2 bonds from topology,
isnt it?

2) If step 1 is correct, the special_bonds command: "special_bonds fene"
(default 0 1 1) will calculate the repulsive LJ interaction included in FENE
potential between 1 and 3 at full strength as lammps knows what molecule is
2 bonds away from topology.

there will be *no* FENE potential between 1 and 3, since there is no
bond between them.
special_bonds doesn't compute anything. it sets a scaling factor.

3) Then if I include a lj/cut to this, then the net potential will count LJ
interactions twice (one from FENE and other from lj/cut) between molecule 1
and 3.

4) If till Step 3 is correct, then it becomes like interactions between
molecule 1 and 3 or molecule 1 and 4 will have contributions from two LJ
terms (FENE and lj/cut) where as interactions between 1 and any other
molecule (5 to N) will have only one LJ term (that is from lj/cut).

Am I making some fundamentally wrong assumption?

yes. bonded potentials are only applied to pairs of atoms that are in
the bond list.
i already said this.

axel.