Dear Lammps Users,
I have conduced an NPT simulation with a box of large molecules using full PBC. Now I want to extend the box in the z-direction to create vacuum on both sides of the molecules. Unfortunately, this will cause molecules to remain broken across the periodic boundary. I need a way to extend the box vectors in the z-direction without fragmenting the molecules for the next simulation.
I have searched for a good way to do this and I’m sure there must be a simple solution but I can’t seem to find it.
Any suggestions? Thanks in advance.
Evan L.
Dear Lammps Users,
I have conduced an NPT simulation with a box of large molecules using full
PBC. Now I want to extend the box in the z-direction to create vacuum on
both sides of the molecules. Unfortunately, this will cause molecules to
remain broken across the periodic boundary. I need a way to extend the box
vectors in the z-direction without fragmenting the molecules for the next
simulation.
I have searched for a good way to do this and I'm sure there must be a
simple solution but I can't seem to find it.
Any suggestions? Thanks in advance.
how about this?
write out your system with:
write_dump all custom orig.dump id xu yu zu
write_data orig.data
then edit the box boundaries as desired in the dump file (only!).
and start a new simulation with "read_data orig.data" but then
override, both, coordinates *and* box using read_dump.
axel.