For a simple LJ 12/6 simulation, I want to have a simple linear polymer chain of LJ beads with size 1( in LJ unit) connected by the FENE bond potential. As the initial condition, I want to have the chain in a helical shape. To do so, I wrote a python script to create a Lammps data file. But, the problem is that I do not which criteria I need to follow when I want to put the centre of the beads on the helix? Should their centres be at least 1 LJ unit separated from each other along the helix?
Thank for your help,
P.S.: I use Mac OSX Catalina so I cannot use VMD and topotools.
See the tools/chain.f code for an example of creating a box of FENE chains.
Or the Pizza,py chain tool for code that does it in Python.
Neither of these would create a helix. But they show you how
to separate beads by distance and angle constraints to
create chains for a FENE model.