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?

  • $\begingroup$ Note: cross-posted on Physics. $\endgroup$
    – rob
    Apr 24, 2022 at 23:45
  • $\begingroup$ I don't do polymers like this, so I am unfamiliar with Kurt Binders formula for LJ energy, particularly since It doens't look like a Lennard Jones function, but anyways, bonds between attached atoms would be handled by V = k(di,i+1 - 3.8)^2 and atoms in different polymers would interact via the Kurt Binder energy function. This is my guess. I am not sure how atoms that were 2 or more atoms apart in the same polymer would interact. I would guess using the Kurt Binder function, certainly not via the quadratic form your professor gave you (maybe two apart could be the quadratic potential) $\endgroup$
    – B. Kelly
    Apr 25, 2022 at 16:07
  • $\begingroup$ I gave my +1 long ago, but just came here to ask whether you've had any luck with this over the last 5+ months? Please update us! $\endgroup$ Oct 4, 2022 at 19:07
  • $\begingroup$ This post appears to be abandoned. It can be reopened if OP addresses questions/suggestions from the comments. $\endgroup$
    – Tyberius
    Oct 30, 2022 at 19:07


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