Dear all,
I am wondering if lammps is able to model and simulate an infinitely long molecule (by replicating the molecule periodically, like a nanotube or a very long DNA strand). One major problem is how to treat the bonded interactions that cross the boundary. It seems that some special periodic boundary conditions may be needed but I can't find the solution in the user manual. I would appreciate any comments on this issue. Thanks.
Jing
Dear Jing,
If you carefully set up your system so that the periodic replication occurs exactly at the box boundary, you can specify that the “first” atoms are bonded to both the “second” atoms and the “last” atoms. You’re right that it’s the bonding that matters, but it shouldn’t be a problem for the system to have the start of the nanotube or DNA strand bonded to its own end. I don’t think you need special periodic boundary conditions; you just need to have a chunk of molecule big enough that the atoms don’t directly interact with their images.
Joanne