Detection of Internal water along MD trajectory

From: James Starlight (
Date: Mon Mar 17 2014 - 04:14:38 CDT

Dear NAMD users!

I've performed md simulation of water soluble protein having
water-assessable channel in its interior. I'd like to perform analysis
of average number of water molecules detected within the protein
interior during MD trajectory with the possible visualization of such
internal water binding sites. Does SASA calculation which I've seen in
vmd could provide me with additional insights? I'd be thankful if you
provide me with some VMD tools suitable for such task.

Many thanks for help,


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