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

Justin A. Lemkul jalemkul at vt.edu
Wed Nov 17 16:07:36 CET 2010

Adwait Mevada wrote:


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


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