I would like to simulate long polymer chains (~100-200 beads per chain) in a box with periodic boundary conditions (in real units). The average diameter of beads is ~7.5 Angstrom. In this setting, to simulate at concentrations 50-200 gram/liter, the system size would be of the order of 10000-100000 beads if a side of the cubic box is 500 angstrom. In this case, a fully stretched chain will interact with its periodic image (end-to-end distance > half Box Length). Does LAMMPS check this situation and print some error OR I need to calculate end-to-end distance within the LAMMPS input script and check whether it crosses the half box length?
Technically, you can have polymer chains that are longer than the box even, for as long as they don’t overlap when wrapped back into the principal box.
When computing interactions, LAMMPS will correctly identify the closest periodic image. LAMMPS is not subject to minimum image conventions.
Polymers from individual, not cross-linked chains, can “crumble” into small “granules” and then the fully stretched length can be very long without having unwanted interactions of parts of a chain with other parts of itself.
So it depends on the specifics of your system and what kind of accuracy of the results you expect whether you need to make your box larger or not.
Thank you so much for the reply. My chains do not overlap in the central simulation box while computing interaction forces because I generated non overlapped initial configurations for each chain. Further, I run the system for a sufficient number of steps with the soft potential. Thus, my equilibration started from dispersed chains within the whole (central) simulation cell while wrapped (not as whole molecules). But I am not sure about this “Technically, you can have polymer chains that are longer than the box even, for as long as they don’t overlap when wrapped back into the principal box” . Do you mean by wrapping back as whole molecules? Can I ask you to elaborate a bit?
the box even, for as long as they don’t overlap when wrapped back into the principal box" . Do you mean by wrapping back as whole molecules? Can I ask you to elaborate a bit?
periodic boundaries are applied on a per-atom basis.