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

[Justin A. Lemkul]

Adwait Mevada wrote:
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>> Message: 4
>> Date: Wed, 17 Nov 2010 15:08:02 -0500
>> From: Vitaly Chaban <vvchaban at gmail.com>
>> Subject: [gmx-users] Re: nve run of carbon nanotube
>> To: gmx-users at gromacs.org
>> Message-ID:
>>     <AANLkTikE4LsexaxkRGoPd7w38nqwn8_jaRkQc_fFngC7 at mail.gmail.com>
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>>
>> Also, as far as I understand, before NVE simulation, one should
>> equilibrate the system in the  NVT ensemble (at the desired T) and
>> only then switch off T-coupling (=NVE).
> so are you suggesting that for the parameters I want to test I should
> fix a temp say 300K, then simulate it (in vaccum) with NVT, see if the
> physical variables equilibrate around experimental values and then go
> switch of T-coupling?
>> Vitaly Chaban
>>
>>
>>>>> I would not say that you tube rotates so vigorously to be
>>>>> suspicious... The tube is also very small. What about trying a bigger
>>>>> one, e.g. with about 1 000 atoms? It should be more inert, if you'd
>>>>> like it to be such.
>>>> ok. I will do that and tell you what happens.
>>>>>
>>>>>> 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
>>>>>
>>>>> So, now the problem becomes why NVE simulation does not preserve
>>>>> system energy. I did not find above what method you used (MDP file)
>>>>> for the LJ interactions. I believe the problem is someplace around
>>>>> this point.
>>>> I do not get you, surely the itp & top files will have the information
>>>> regarding
>>>> the LJ interactions. As far as i remember for C-C interactions I 
>>>> have C6
>>>> and C12 interaction mentioned in [non_bond param] section and also when
>>>> defining the atom type C I have used the same parameter values, is 
>>>> there
>>>> anything else i have to take into consideration besides that?
>>>> -Adwait
>>>
>>> You didn't set "vdwtype" in your .mdp file, but in this case it  
>>> should default
>>> to "cutoff," which I don't think is a problem.  What might be an  
>>> issue is your
>>> treatment of PBC.  If your box is somewhat small, your system will  
>>> experience
>>> repulsion from forces derived from periodic copies of your  molecule. 
>>>  The proper
>>> approach for a vacuum simulation would be to set "pbc = no" and set 
>>>  all cutoffs
>>> to 0 to capture all intramolecular interactions.
>>>
>>> -Justin
>>
> Justin as you suggested I set pbc=no, but i could not set cutoff's to 0
> as grompp was giving an error saying rvdw>=rlist so i set cutoff for vdw
> to 0.4 instead of 1 which resulted in greatly reduced perturbations in 
> the geometry to the extent that the carbon nanotube retained its 
> cylindrical structure. The temprature was 4K and T.E. of the system were 
> 11 as computed
> by g_energy with LJ being -0.69. setting comm_mode = angular removed any 
> rotation about x axis for the system
> 
> I also tried the same thing with a large nanotube containing 1000 atoms
> as suggested by Vitaly, and his suggestion also works out i do not find
> distortions in the geometry except that being a long narrow tube it 
> flutuates
> along its length, which is fine i suppose.
> 
> What i wonder is why reduction in rvdw helps in reducing the fluction?
> and also now if i want to put this carbon nanotube in water will using 
> this parameter set suffice or i will have to make changes so that it is 
> stable in
> water either in NVT or NPT ensemble?
> 

Making ad hoc changes to rvdw will break whatever force field parameter set 
you're using.  For vacuum, you should set all cutoffs (rvdw, rcoulomb, rlist) 
equal to zero.  I suspect that the reduced rvdw is masking the real underlying 
physical instability.

As for the condensed phase parameters, sensible non-zero values of all cutoffs 
would be required, per whatever force field you're using.

-Justin

> 
> -Adwait
> 
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-- 
========================================

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

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