[gmx-users] Unstable Carbon Nanotube

[Bob Johnson]

Hello,
I am currently simulating a single carbon nanotube to verify that I have a
correct force field. Based on advice found on the GROMACS Mailing List I am
performing simulations where only bonded interactions are calculated, another
where bonded and angle interactions are calculated, and so on. Performing the
simulations with only the bonded interactions still results in a mess: the
nanotube collapses on itself and becomes this amorphous cylinder. The energy
and temperature during the simulation are fine. This is a very strange result
to me. The bonded interactions are as follows:
Morse Potential
D = 478.9 kJ/mol
r_0 = 0.1418 nm
gamma = 21.867 nm^-1

It seems that this potential should produce a fairly rigid structure. However,
that's not what I'm seeing here. Any suggestions?
Thanks,
Bob