Dear Lammps users
I am trying to simulate polymer model where bonds between polymer beads are modelled using FENE potential.
I am using Rmax coefficient to be 1.2 in lj units but I am getting problems in defining initial bond length and getting an error fene bond too long.
From archives I found out that for Rmax to be 1.5 ,equilibrium bond length should be about 0.97 (http://lammps.sandia.gov/threads/msg67723.html).
So is there any way of predicting equilibrium bond length for different Rmax values.
Can you please help me out in resolving this problem.
Thanks and regards
Mrityunjay Samanta
Dear Mrityunjay,
Hello Mrityunjay. First, the FENE potential in LAMMPS is actually the summation of the attractive FENE and the repulsive portion of the LJ potential. The pairwise equilibrium distance of this FENE (plus the repulsive LJ Potential) is 0.96 which can be obtained by taking the derivative of the FENE equation and setting it equal to zero. The FENE equation is given here where it states fene bond style: http://lammps.sandia.gov/doc/bond_fene.html
Instead of having just two beads, the equilibrium bond length for a system of polymer beads would either slightly deviate from 0.96. The level of deviation would depend on the number of beads you have. In my case, I have FENE bonds (with cutoff distance of 1.5) and repulsive LJ potential acting between non-connected beads. Therefore, my equilibrium distance for my system hovered around 0.97.
I believe that predicting the equilibrium bond length for different cutoff distance (Rmax) and fene bond too long error are two different issues. FENE bond too long results in many different situations as a consequence of bad MD trajectories. Which part of your simulation are you receiving this message? Thank you
Sincerely,
Masato Koizumi