So using various tools (especially topo-tools) it is very-well possible to replicate monomer units to ‘create’ a chain. However to generate many such chains such that the chains are entangled, and yet packed in space such that relatively small computation time is sufficient to bring them to a well equilibrated state, we need a good starting condition. Random walks have been shown to contain bias.
Research papers (pubs.acs.org/doi/pdf/10.1021/ma00031a031) state that models generated with phantom chain growth method are a better starting point than random walk models.
How can I generate chains, based on the phantom chain model? I was unable to find any access to any phantom chain generation algorithms as such. Do I create a linear chain then apply transformation matrices to chain segments? If so, what transformation matrices do I apply?
(If I am asking in the wrong place, please let me know. Before I can proceed to MD in LAMMPS, I need a good starting configuration of my melt. Hence asking here)
Brahm Prakash Mishra
National Institute of Technology, Trichy
How can I generate chains, based on the phantom chain model?
Ask the authors of the papers is they have a code they
are willing to give you?
Hi, Brahm. That’s a very old, outdated paper you linked. See for example Steve’s own J. Chem. Phys. with Rolf Auhl, Gary Grest and Kurt Kremer from 2003. This “double bridging” method is integrated into LAMMPS as fix bond/swap. Also, for generating initial chains, you get faster equilibration if you match the typical bond angle theta to the chain stiffness C_inf (if you know it) as C_inf = <1+cos(theta)>/<1 - cos(theta)> than just to use completely random walks (which have C_inf = 1).
I see. So better equilibration methods are available, I went to that. Thanks for the double bridging method.
You said typical bond angle to chain stiffness is to be matched to the bond angle. Now chain stiffness we can calculate from experiment right? Also, given a certain theta, I pick up points at that angle?
I am very confused about random walks. Which will be a good literature to search and learn about modelling polymers on random walks with chain stiffness?
Brahm Prakash Mishra
Monte Carlo and Molecular Dynamics Simulations in Polymer Science by Binder might be of use although it is an older text now.