[gmx-users] program crashed

Dongsheng Zhang dong at pampas.chem.purdue.edu
Tue Jul 4 07:29:17 CEST 2006


Thank you for your reply. EM works fine before position-restrained MD.
Do you have any other suggestion besides to reduce the number of water
inside the nanotube? Thanks!


On Tue, 2006-07-04 at 15:23 +1000, Mark Abraham wrote:
> 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
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