From: Charles Zhao (cicero225_at_yahoo.com)
Date: Wed Aug 11 2010 - 01:32:52 CDT
I constructed a group of similar solvated protein systems in periodic box
boundary conditions using the exact same procedure. Then I ran them all in namd
2.7b2 for 10ns using virtually identical configuration files (I literally
copy/pasted, changed the filenames, and changed the periodic box sizes to
properly match the system).
The problem is, now I have some systems where the solvent congeals into this
sphere shape (with a few waters flying off into the distance), and others where
it stays in the proper shape of a box. The only thing I can think of is that
the water density is somehow too low in the sphere systems. But then why is it
perfectly fine in the remaining systems? They're all of similar size, differing
perhaps by 30 or so angstroms in various dimensions, and constructed by the same
method. And since when does water in a periodic box system, no matter how low
the pressure, decide to form a sphere in the middle?
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