[gmx-users] deformation in structure of carbon nanotube

[kordzadeh at aut.ac.ir]

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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