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

[Vitaly Chaban]

>  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.


> 3) temprature keeps on rising as the simulation proceeds is this all right?

No. For how much does it increase?


--
Dr. Vitaly Chaban