[gmx-users] program crashed

Dongsheng Zhang dong at pampas.chem.purdue.edu
Tue Jul 4 07:02:20 CEST 2006

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

All the best!


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