VMD-L Mailing List

From: Clement Fang Jin Koh (cfk2120_at_columbia.edu)
Date: Wed Aug 11 2021 - 12:32:56 CDT

Hi VMD team,

I have a LAMMPS data file of a forming network that is not yet a gel,
created using fix bond/create in LAMMPS from a system starting with
monomers. I'm trying to measure the radius of gyration of the various
fragments created using "measure rgyr" but have been unsuccessful in
joining the fragments using pbc join. The closest I've gotten to getting
the whole fragments together is by using pbc wrap -all followed by pbc join
fragment -sel "fragment X", but it still fails in some cases. Does anyone
have any suggestions?

Thanks,
Clement

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