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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