Hi all,
I am hoping to replicate the persistence length of a polymer using a CG model. I would like to use a FENE potential for the bonded pairs, but scale down the LJ and coulombic interactions to 0.3 between 1-3 and 1-4 pairs in my polymer chain. I use special_bonds as shown below to achieve this. Nonetheless, the output shows the special bonds to be 0,1,1 from the fene potential. Could someone help me identify the issue or point me in the direction to achieve this scaling while defining my bonded pair with a fene potential?
snippet from input file:
pair_style hybrid lj/cut/coul/debye 0.906 2.5 8.0 lj/expand 2.5
bond_style fene
special_bonds lj 0.0 0.3 0.3 coul 0.0 0.3 0.3
snippet from log file:
WARNING: Use special bonds = 0,1,1 with bond style fene (src/src/MOLECULE/bond_fene.cpp:186)
Where?
This is not showing the special_bonds setting, but a warning from the FENE bond style that it is supposed to be used with special_bonds lj/coul 0 1 1. Nothing stops you from ignoring this warnings, but you must also be aware that you are on thin ice when using a setting that goes against the recommendation and that it may have unintended consequences.
Thank you for your response!
I misunderstood the warning mostly because when visualizing the polymer chain, I realized that scaling down the 1-3, 1-4 lj/coul interactions did not change the persistence length of the polymer. I tried using special_bonds lj/coul 0 0 0 as a test, with no significant changes to the persistence length of the chain either. Was I incorrect to interpret that if each bead carries a charge, by scaling down these interactions the chain would be less extended?
This is not a LAMMPS issue, but a question about the science and thus something you need to discuss with someone that cares about your research, like your adviser or tutor or similar.