[gmx-users] Water clustering

[H T]

Hi, I am trying to calculate micelle formation with SDS molecules for 
all-atom simulation.
49 SDS monomers (will increase it later) were settled in 15nm x 15nm x 15nm 
box.
And I put water molecules from spc216.gro to the box.
Considering water density is 1g/ml, around 112800 molecules are required but 
only 3400 water molecules was settled (around 3%) with genbox command at 
maximum. With this configuration, the SDS molecules assemble but also water 
cluster appeared. After 100ps MD, there is a room occupied with no atoms 
(vacuum, phase separation) and it is a bit funny. (1) Increasing the number 
of water to a realistic value or (2) tuning the parameter to avoid spc water 
aggregation might be good, but I don't know how to do that. Please give me a 
rope for it. Thanks,

taka 
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