Quoting Vitaly Chaban <[email protected]>:
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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