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

Alex nedomacho at gmail.com
Sun Oct 8 23:53:32 CEST 2017

I just replied to Neha's post. You are having issues that have nothing 
to do with Gromacs, i.e. Gromacs is simply responding to incorrect 
system setup. Please generate a proper periodic topology and use a 
PBC-compatible box.


On 10/8/2017 3:47 PM, Ming Tang wrote:
> 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

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