[gmx-users] How to perform simulation of carbon nanotube in GROMACS in NPT ensemble?

[Ming Tang]

Dear list,

I have gone through carbon nanotube guide on GROMACS website.
http://www.gromacs.org/Documentation/How-tos/Carbon_Nanotube<https://www.researchgate.net/deref/http%3A%2F%2Fwww.gromacs.org%2FDocumentation%2FHow-tos%2FCarbon_Nanotube>
I have a nanotube aligned to z-direction. I am trying to simulate infinite nanotube using periodic conditions. There are issues while simulating this system when pressure coupling is used.

GROMACS or other mailing list doesn't provide mdp files for simulation of carbon nanotube using NPT ensemble. It appears that we cannot freeze groups to constrain nanotube in NPT ensemble. We might have to use position restraints for nanotube (most papers report this). I have imposed position restraints on nanotube and in doing so, the z coordinates fluctuates by 0.5-1 nm in Z direction. This is not an issue with NVT simulation.

How do I equilibrate nanotube system using pressure coupling for nonotube/graphene etc with infinite long surface? Should we use semi-isotropic scheme (not apply pressure along the axis of nanotube) for pressure coupling or it should be isotropic?

P.S.: the force field is opls based on gromacs tutorial and GROMACS version is 5.1.4. Temperature coupling -V-rescale

Thanks,
Ming on behalf of Neha