Dear all,
I have a few questions regarding the solvateBox command.
1. Is there any rule or guide in setting the distance value for
solvateBox? From the tutorial, i understand that the distance value
will put all the atoms of the solute to be at least the distance value
from the edge of the water box.
2. How does this distance value relates to the periodic boundary
conditions, cutoff and box size applied in the system? I understand
that the cutoff to be used must not be larger than half the smallest
box dimension.
3. If i want to solvate the system with TIP3P waters, with minimum
distance of 20A between the protein-membrane system and the boundary
of the periodic box, how can i do it with the solvateBox command?
Pls advice. Thank you very much!
Regards,
Colvin
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Received on Mon Aug 23 2010 - 18:30:07 PDT
