[gmx-users] how to set domain decomposition for inhomogeneous systems?

[Mark Abraham]

On 4/09/2011 7:37 PM, zhongjin wrote:
> Dear GMX user,
>       I am using GMX4.5.4 (double precision) to simulate electrolyte 
> confined in a CNT with polarizable model. The CNT diameter is 3.0 nm 
> and length is 6.0 nm. The box is 5.0*5.0 *6.0, out of CNT is nothing, 
> that is to say, the system is inhomogeneous,please see it by clicking 
> this link http://photo.163.com/hzj1000/list/#aid=228653982&m=0&page=1 
> <http://photo.163.com/hzj1000/list/#aid=228653982&m=0&page=1>
>

I think all your runs are broken, because as your potential energy is 
always large and positive. Check out 
http://www.gromacs.org/Documentation/Terminology/Blowing_Up.

Mark
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