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

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 18 00:54:58 CET 2010

Adwait Mevada wrote:
> Quoting gmx-users-request at gromacs.org:
>> Send gmx-users mailing list submissions to
>>     gmx-users at gromacs.org
>> To subscribe or unsubscribe via the World Wide Web, visit
>>     http://lists.gromacs.org/mailman/listinfo/gmx-users
>> or, via email, send a message with subject or body 'help' to
>>     gmx-users-request at gromacs.org
>> You can reach the person managing the list at
>>     gmx-users-owner at gromacs.org
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of gmx-users digest..."
>> 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>
>> Content-Type: text/plain; charset=ISO-8859-1
>> 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.


> -Adwait
> ----------------------------------------------------------------
> This message was sent using IMP, the Internet Messaging Program.


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


More information about the gromacs.org_gmx-users mailing list