[gmx-users] (no subject)

[Mark Abraham]

wuxiao wrote:
> Dear Mark,

Please use a descriptive Subject: line for your emails.

>   Thank you very much for the quick reply. According to your 
> suggesstion, I had a look at the structure or trajectory using ngmx. 
> Only to find that there are some big hole in the center, which seems to 
> indicate the system is very inhomogeneous. 

OK - check for periodicity effects, however.

>And the system 
> volume  decreased slowly.  when I using cutoff instead of PME for 
> columbic force, and change the cutoff from 1.4 to 1.0, the mdrun 
> finished 300 ps successfully. Another 3ns is started to try whether it 
> can succeed too. more help from these descriptions?

I think you should find out why your starting structure had this big
hole you report, else you're likely to keep running into the problem
because you keep using the same erroneous method :-)

Mark