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<DIV><FONT face="MS UI Gothic" size=2>Hi, I am trying to calculate micelle
formation with SDS molecules for all-atom simulation.</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2>49 SDS monomers (will increase it
later) were settled in 15nm x 15nm x 15nm box.</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2>And </FONT><FONT face="MS UI Gothic"
size=2>I put water molecules from spc216.gro to the box.</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2>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,</FONT></DIV>
<DIV><FONT face="MS UI Gothic" size=2></FONT> </DIV>
<DIV><FONT face="MS UI Gothic" size=2>taka</FONT></DIV></BODY></HTML>