[gmx-users] Water clustering

H T takayama at ceres.ocn.ne.jp
Fri Jul 10 16:32:51 CEST 2009

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 
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,

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20090710/f32e8544/attachment.html>

More information about the gromacs.org_gmx-users mailing list