Dear Lammps community,
Is there a convenient way to wrap whole molecules in a periodic box, not allowing bonds to span the boundaries? For example, wrapping a particular atom or COM of a molecule, and moving the rest of the atoms in the molecule to that location.
I think this is what owrap does in the pizza.py tool? I tried using owrap, but I can get following error:
** d3zis2.lammpstrj contains dump file of atom type
** d3zis3.lammpstrj, I have tried with column of dump type “id” and “mol” for same results
read 1 snapshots
1 snapshots selected out of 1
assigned columns: id type x y z
Unscaling dump …
Wrapping to other …
Traceback (most recent call last):
File “”, line 1, in ?
File “/home/hhatch/software/pizza-8Dec09/src/dump.py”, line 538, in owrap
ix = self.names[“ix”]