[gmx-users] Pore Size

[Sanket Ghawali]

 Hi lists,

I have performed a md simulation of peptides in sds micelle for 100ns. The
peptides move to the interface after a time interval of 30 ns and remains
there till 100ns. After visualizing it in VMD i see a pore formation in sds
near the interface where the peptide is. I also see water molecules
entering the hole surrounding the peptide. I wish to calculate the pore
depth.

Any suggestions on how to go about doing this?
-- 
Sanket