[lammps-users] Exclusion List

Hi Everyone,

I am running a simple simulation where I have 60 molecules and each molecule has 2 types of atoms, type 1 and type 2.
I am trying to exclude pairwise interactions between atoms in the same molecule (intramolecular), but I need pairwise interactions between atoms in different molecules (intermolecular).
I couldn't figure out how to do this. Since there is no combined molecule id and type exclusion option in "neigh_modify exclude".

Something like this : "neigh_modify exclude molecule 1 type 1 1" (it doesn't exist)
if I use "neigh_modify exclude type 1 1", it will exclude intermolecular interaction as well.

Do you know any way of excluding intramolecular pairwise interactions without excluding intermolecular ones ?

Thanks in advance,

If your molecules are small (linear chains of up to 4 atoms), you should be
able to use the special_bonds command to achieve this.

Hope this helps,


Molecules are not linear chains, some atoms have 4-5 bonds and molecules have total 28 atoms.
I don't think that the special bonds is going to work.

Thanks anyways,

As is mentioned in the manual:
“The exclude molecule option turns off the interaction if both atoms are in the specified group and in the same molecule, as determined by their molecule ID”
I think something like:" neigh_modify exclude molecule groupID " maybe what you want.
Just a suggestion, I haven’t tried it.

Yes I tried this it works but it has a limitation. The maximum group you can create is 32. I have 60 molecules.


If you put all your molecules in one group and use

neigh_modify exclude moleclue group-ID

then all pair-pair interactions within each moleclue
will be excluded, assuming the atoms of the molecule are in the
group. Pair interactions between atoms in different moleclues
will still be on. Is that what you want?


Yes I got it now.

Thanks a lot,