Problem in Simulating a Chain Molecule

Hi everyone,

I met a problem in simulating a chain molecule in LAMMPS.

As is shown in the input script “in.polymer” as attached, I created only one molecule in which two atoms were connected by a FENE bond in the simulation box with periodic boundary condition. The template of the molecule is attached as “straight_line.molecule”. After creating the molecule, I minimized the energy of the system.

However, as long as I set the distance between the two atoms smaller than R0(=1.5sigma) in the FENE potential, there would be “segmentation fault” during the simulation. If the distance between the two atoms was larger than the cut-off distance of the L-J potential, there would not be “segmentation fault” and I could get a configuration of the system in the end (though the atoms did not move at all which is reasonable). This at least proved that the template “straight_line.molecule” could be used to create the molecule without problems. I learnt from previous thread in the LAMMPS mailing list that this kind of “segmentation fault” might be caused by a bad input configuration. However, even if I set the distance between the two atoms near the equilibrium distance of the potential (0.96sigma), there would still be this “segmentation fault”. Also, I believe that this input configuration of only two atoms connected by a bond is the simplest among all, so I really can’t find a reason for this problem.

Does anyone know how to solve this problem?

Thank you in advance,

Fan Yang

in.polymer (548 Bytes)

straight_line.molecule (145 Bytes)

Your molecule template file needs these sections:

Special Bond Counts

1 1 0 0
2 1 0 0

Special Bonds

1 2
2 1

to exclude bonded interactions correctly. LAMMPS should issue
a warning or error if that section is missing for a molecule with bonds.

I’ll add it.