[gmx-users] deformation in carbon nanotube structure

Alex nedomacho at gmail.com
Fri Mar 16 06:00:11 CET 2018

There's a good reason noone replied when you posted this question the 
first time: noone knows what paper, noone knows what that "little 
deformation" is, and, most importantly, it has nothing to do with Gromacs.

Andrea Minoia wrote a very reasonable tutorial http://bfy.tw/H8rY , 
which, if followed properly, guarantees basic mechanics of CNTs and 
graphene. If you need to refine the model with parameters you find in 
literature, said tutorial gives complete information on how to proceed.


On 3/15/2018 10:25 PM, kordzadeh at aut.ac.ir wrote:
> Hi every one
> I want to investigate carbon nanotube, because my CNT is large I couldn't get topology from automatic servers, then I used gmx X2top to make topology and I corrected bond and angle constant with data from paper, in first part of my simulation I don't apply any restraint on CNT because I want to investigate real behaviour in solution
> then I want to investigate CNT as the absorber, I applied restraint,
> but I have a problem, after the run when I saw CNT in VMD, a little deformation occurred in structure and tubular shape is changed but when I ran a system with the pure topology that gmx x2top produced this problem didn't occur,
> if it is necessary I can tell more detail about the correction that I did in topology.
> Is this deformation meaning wrong in my simulation or I can ignore it?
> when I applied restraint , this problem didn't occur with corrected topology and x2top topology.
> Please guide me about this problem
> Thank you very much
> Regards
> Azadeh

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