6 votes

Benchmarking Monte Carlo simulations of polymers

Alot of the early pioneering in Monte Carlo (MC) moves were done initially using lattices. While I am not directly aware of places to look for benchmarks, the pioneers in the 90's for Monte Carlo ...
  • 1,030
4 votes

What formula should I use to calculate the total energy of a linear polymer chain?

The difference between total potential energy and total energy is just the kinetic energy, which is the sum of the kinetic energies of your particles, $$E_K = \frac{1}{2}\sum_{i=1}^3 m_i v_i^2$$ where ...
  • 613
3 votes
Accepted

How should I calculate total potential in a polymer chain?

You'll want to add up all interactions that you can, up to some appropriately chosen cutoff distance. Choose the VDW cutoff such that the total energy doesn't change much if you further increase this ...
  • 613
2 votes

How do I calculate the acceptance criterion for configuration bias sampling of my polymer?

From my little experience I would start by defining a spin value for "this site has solvent instead of polymer". (It could replace your existing "no polymer here" spin value, or be ...
2 votes

How to generate a polymer in different conformations?

You could try to run a GROMACS simulation with COLVARS, which takes the radius of gyration as a possible collective variable. Running an umbrella sampling simulation with a suitable set of weights ...
2 votes
Accepted

Discrete lattice polymer simulations

Ironically, there exist no on-lattice software for such a Flory-Huggins software. This is primarily because there are no set standards for running such simulations! Most people run their own DIY code ...
  • 4,019
1 vote

End-to-end correlation of polymers not decorrelating

The problem with this moveset is that it is too local. The best way to decorrelate polymer configurations is to run simulations with more aggressive moves, such as chain regrowth.
  • 4,019
1 vote

How to check for phase separation in polymer simulations?

Turns out the best way to spot phase transitions in polymers is to run the extended cell simulations and calculate surface tension, as seen in this paper: http://dx.doi.org/10.1063/1.3227905.
  • 4,019

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