Is there a better way to carry out Primitive Path Analysis by Kremer-Grest model?

Hello everyone!

I’m very thankful to who answer my question

Kremer-Grest(KG) model is a successful bead-spring model in polymer physics(JCP,1990,92,5057)

In 2005, they present Primitive Path Analysis(PPA) method to get the entanglement length in KG model(Polym. Phys., 2005,43,917)

Specifically, the intrachain excluded-volume interactions are disabled, whereas the interchain excluded-volumeis retained

Excluded-volume interactions in KG model is LJ potentials

However, in the lammps, bond/FENE comand contains the LJ potentials between two bonded atoms

This partial potential in bond/FENE comand should be disabled

I didn’t find a command could do this, including special_bond command

I find a way is that:

In the src/bond_fene.cpp, I could comment on these code:
// force from LJ term

if (rsq < TWO_1_3sigma[type]sigma[type]) {
sr2 = sigma[type]sigma[type]/rsq;
sr6 = sr2
fbond += 48.0

So, LJ poteneial is none(Energy is not important in PPA)

My question is :

1)Is the method Ok?(I’m not good at C++)
2)Can we do this by some commad in scrpit?

Best wishes,

Yongjin Ruan

I believe that should remove the LJ force from the FENE bond.
However that is the repulsive portion of the bond, so not
clear what will keep your 2 bonded atoms from collapsing
on top of each other? Those 2 atoms have no pairwise
LJ term b/c of the special_bonds exclusion.