Recently, I applied lammps (17 Oct 2012 version) to calculate the lattice thermal conductivity of infinite polymer crystal. My simulation box was built by replicating unit cell to form a supercell. This supercell is the simulation box. My force field is General Amber and periodic boundary condition was set in the three directions.
Because my simulation system is the infinite polymer crystal, it is necessary to build a bond to go across the box boundary. But during my simulation, the error, Bond/angle/dihedral extent > half of periodic box length, always occurs. Then the simulation stops. So I am very confused that (i)Was there something wrong with my modeling process, leading to my initial structure going wrong? (ii) For this version of lammps, does minimum image principle still work? If it works, I think that the atom and its image in the neighboring box will be bonded instead of the two atoms in the two end of the box.
Did you get a warning about inconsistent image flags?
How big is your simulation box in each periodic dimension?
The error you list should also have been a warning,
not an error. But it indicates you should make your
periodic box bigger when you have a system where the
bonds loop around in a periodic sense.
If you are getting errors, not warnings - I believe
you do not have the current version of LAMMPS?
I didn’t get the warning about inconsistent flags. My simulation box is 30, 15.74 and 7.6 angstrom respectively. This is a 1x2x1 supercell of the polymer crystal. I have tried to enlarge my box dimension to about 100 angstrom in the three directions. In that case, the simulation could run normally. But this situation is not what I want, Because the polymer chain forms a loop not a infinite polymer crystal. The version of lammps I used is 17 Oct 2012, and ‘Bond/angle/dihedral extent > half of periodic box length’ in the output file is indeed an error not a warning.
I didn’t get the warning about inconsistent flags. My simulation box is 30, 15.74 and 7.6 angstrom respectively. This is a 1x2x1 supercell of the polymer crystal. I have tried to enlarge my box dimension to about 100 angstrom in the three directions. In that case, the simulation could run normally. But this situation is not what I want, Because the polymer chain forms a loop not a infinite polymer crystal. The version of lammps I used is 17 Oct 2012, and ‘Bond/angle/dihedral extent > half of periodic box length’ in the output file is indeed an error not a warning.
Please update your lammps version. The treatment of bonds has been made more consistent since two years ago.