I need to simulate the off-lattice movement of a polymer chain in a 3D space using Monte Carlo simulation. Note this is not a simulation of polymer growth; rather this is about polymer movement/motion.
My polymer is 30 units long, and it should use the bead-spring model.
From the Page-148 of the book Applications of the Monte Carlo Method in Statistical Physics by K. Binder, I know that bead-spring models use the following Lennard-Jones energy function:
$$V(r)= \begin{cases} -V_0\ln\big(1-(\frac{r}{r_0})^2)&; r_0\ge r\\ 0&; r_0\lt r \end{cases} $$
On the other hand, my professor gave me another function called harmonic spring energy function and told me that I need to use that in combination with the Lennard-Jones energy function:
Then the energy of each spring between atoms $i$ and $i+1$ = $V=k(d_{i, i+1} - 3.8)^2$
Where should I apply this function exactly?
