[gmx-users] program crashed

[Mark Abraham]

Dongsheng Zhang wrote:
> Dear GMX users,
> 
> I am studying a system of a capped nanotube with a polymer in water.
> When I use genbox, some water will be inside of the nanotube. This might
> cause bad contact of water molecules inside of nanotube. Does anyone
> know how to control the total number of water molecules inside the
> nanotube? In general, could someone give me suggestion how to prevent
> the program crash because of bad contacts? I am having this problem now.
> I have tried to use position constraint to relax water and heat the
> system from 100K. It doesn't help. Any suggestion will be highly
> appreciated.

Identify the waters inside the tube, go through the .gro file and delete 
them manually. Then edit accordingly the number of water molecules in 
the groups at the bottom of the .top file. Minimise before doing 
position-restrained MD, too.

Mark