[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.
>>
>
> Flexible water should not be used for MD.

what do you mean?


>All the water models in Gromacs
> should be rigid.  As such, "define = -DFLEXIBLE" is incorrect.

where did water come from? he said "I am simulating a carbon nanotube
in vaccum (NVE ensemble)"


>>> 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?
>>
>
> Using a plain cutoff for the electrostatics could be causing this.
>
> -Justin
>
>>
>> --
>> Dr. Vitaly Chaban
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>