I would like to find the radius of gyration and the end to end distance of all the chains to check for equilibration. but i need the unwrapped coordinates to do that. Is there a way to store the unwrapped coordinates or if I dump x y and z, are they unwrapped?
Can you help me with a package that can evaluate the rg^2 (radius of gyration), re^2 (end to end distance) and the end to edn auto correlation function for all the chains using lammps output.
You can dump x,y,z with image flags (see dump_modify or dump custom),
so that the unwrapped position can be computed from
x + boxsize * imageflag. The Pizza.py dump tool will do
the unwrapping for you. I suppose we could make an option
to dump x,y,z unwrapped from LAMMPS itself.
You'll need to post-process the values to compute Rg of end-to-end
for individual molecules with your own code, or add a tool to
Pizza.py. The fix_spring_rg.cpp file in LAMMPS has some code that
computes a Rg for a spring constraint ... so you could look at that to
see how it's done.