[gmx-users] Carbon Nanotube Unstable with LJ

[Bob Johnson]

Hello everyone,

I am simulating an infinite nanotube. The force field for the bonds, angles, and
dihedrals seems to produce a stable tube. However, when I include the LJ
interactions the tube forms kinks and relaxes into a different structure. I've
tried getting the LJ pairs from the pair list in the topology file as well as
from the Generate Pairs option. Although, I'm not 100% sure what the Generate
Pairs option does. In both cases I'm setting nrexcl to 3. I figured that the
Generate Pairs option creates LJ pairs for atoms that are separated by 3 (the
nrexcl setting) bonds. What does the FudgeLJ feature do and when would you want
to use it?

My topology was generated in x2top and it seems that the periodic boundary
conditions are set correctly. The LJ parameters are the following:
c6 = 5.7353e-3
c12 = 1.8707e-5

Thanks,
Bob Johnson