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

[Justin A. Lemkul]

Vitaly Chaban wrote:
>>>>  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?
> 

http://lists.gromacs.org/pipermail/gmx-users/2008-October/037571.html

> 
>> 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)"
> 

Sorry, missed that part.  I saw the "define" line and assumed some incorrect 
treatment of water.  I guess that probably invalidates my point below, as well.

-Justin

> 
>>>> 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
>>
>> ========================================
>>
> 

-- 
========================================

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

========================================