Periodic-molecules and periodic conditions

User discussions
1

GROMACS version:
GROMACS modification: No
Hello, I’m reading a paper where they used the below settings in their simulation:

cut-off scheme (Verlet: particle based cut-offs)
cutoff-scheme = verlet
; nblist update frequency
nstlist = 20
ns_type = grid
; Periodic boundary conditions: xyz, no, xy
pbc = xyz
periodic-molecules = no
; Allowed energy error due to the Verlet buffer in kJ/mol/ps per atom,
; a value of -1 means: use rlist
verlet-buffer-tolerance = 0.005
; nblist cut-off
rlist = 0.9
; long-range cut-off for switched potentials

The point I don’t understand is:
what does “Periodic boundary conditions: xyz, no, xy” mean, are there three kinds of boundary conditions in this simulation?
Besides, they also used “periodic-molecules = no”, Is it physical? Because bonds could be broken if any molecule goes through the boundary.

Appreciated for any help.

2

Hi,
it is commented, look at “;”.
Plus, xyz means that in all directions you have PBC, while xy is just along xy directions. Note, “xy” is only used when you have walls at the end of your box depending on what you wanna do.

3

periodic-molecules = no is what you are usually using, and it is the default. Setting it to yes means that there are periodic molecules, such as polymers, i.e., that the molecule itself is getting repeated across the periodic boundary.