From: M K (
Date: Sat Feb 06 2016 - 07:23:08 CST


I intend to output the final frame of a periodic system to a non-periodic
form in VMD and then export it as a lammps data file (topo tools) and use
it in a non-periodic simulation study in lammps.

I use "pbc wrap" on the last frame, followed by this command:

pbc join fragment -bondlist

However, there is still one bond overstretched along the cell, which makes
problem later in the lammps data file output. Also the angles corresponding
to those two atoms produce errors of lammps at step 0 (lammps user may find
this useful: Bond atoms 718 733 missing on proc 1 at step 0) (This is
obvious since there is not periodic boundaries anymore).

Can you pleas help me with this issue, making a good output useful for the
non-periodic simulation? Any suggestion/solution is appreciated.