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

[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.

> 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.

--
Dr. Vitaly Chaban