[gmx-users] Re: nve run of carbon nanotube

[Adwait Mevada]

Quoting Vitaly Chaban <vvchaban at gmail.com>:

>>  Dear Gmx-users,
>>  I am simulating a carbon nanotube in vaccum (NVE ensemble). I have taken
>>  parameters of carbon nanotube from "Strong correlations and Fickian
>> water water
>> diffusion in narrow carbon nanotube, Biswaroop Mukherjee, Prabal K.
>> Maiti Chandan
>> Dasgupta and A. K. Sood, JCP, 126 124704 (2007)".
>> During the run my carbon nanotube does not remain cylindrical, it
>> bends inwards and forms
>> a dumbell shaped structure, also it rotates in space and does not
>> remain fixed.
>> My questions are
>> 1) are my itp and mdp parameters correct
>
> Formally correct.
>
>
>> 2) how do i determine if system is really in ground state or stable
>
> You CNT should not migrate within a box, for sure. I believe it is
> principally impossible in spite of the force field parameters that can
> be used. You may want to upload the video with the system dynamics on
> the YOUTUBE for us to look at.
>
hope this might be useful:
they are top and sideviews
http://www.youtube.com/watch?v=aMMa4o0CzxU
http://www.youtube.com/watch?v=UVksVaHcw8U
http://www.youtube.com/watch?v=xJu3NSkA3gU
http://www.youtube.com/watch?v=cdcyqnPY7D4
>
>> 3) temprature keeps on rising as the simulation proceeds is this all right?
>
> No. For how much does it increase?
>
I am sorry by mistake I took the total energy which was rising as temprature!

well upto first 30ps the temprature remains at 2K and then it jumps to  
a range of 25-40K in which it flucutates in the whole simulation,  
though there is a slow rise like 1K/100 ps from the plot.
the total energy is rising at a rate of 1.8 kJ/mol for 100ps based on  
the plot I am seeing.
Thanks for helping me out.
>
> --
> Dr. Vitaly Chaban
>



-Adwait

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