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

Vitaly Chaban vvchaban at gmail.com
Wed Nov 17 21:08:02 CET 2010

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).

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

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