[gmx-users] Simulation of Carbon Nanotubes with bending deformities

Jashimuddin Ashraf jashimuddin.ashraf23 at gmail.com
Sun May 17 17:28:31 CEST 2015

Dear gromacs users,

I am simulating carbon nanotubes in GROMACS. So far I have only simulated
straight CNTs. Now I'd also like to simulate CNTs with bending deformities.
I have generated a bent .pdb of my nanotube structure and the simulation
runs without any error (I have run the energy minimization and the
structure after energy minimization is quite okay).

But my problem is as soon as I run the simulation, the bent CNT goes
straight within a few pico seconds. Is this because of my forcefield (I
have only considered a bond length of 0.1418 nm in my forcefield.itp file)?
How can I solve this problem?

Thanks in advance.

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