[gmx-users] Range checking error

[Mark Abraham]

Yanzi Zhou wrote:
> Thank you.
> I recompiled the software with gcc, but my job still crashed at about 
> 170ps. I tried 1 ns simulation for 1PGB in water downloaded from 
> http://www.dddc.ac.cn/embo04/practicals/9_14_1.htm, it can be finished. 
> But when I tried to do NTP simulation of DPPC from the benchmarks of 
> Gromacs, my job died on 6 processes with double precision gromacs.  I 
> found the job crashed when I:
> do NTP simulation for a large system, and
> use PME
> on more than two processors with double precision gromacs.
> 
> 
>>> Make sure your system is properly energy-minimized and that the 
>>> potential
>>>
>>> energy seems reasonable before trying again.

What have you done to check that your system preparation protocol is 
reasonable?

Mark