AMBER: box size in explicit water

From: Lwin, ThuZar <>
Date: Wed, 6 Jul 2005 11:39:47 -0500

Dear Amber users,
    I have a protein that is 50Angstrom in diameter and I would like to solvate it.
So I did

solvateOct protein TIP3PBOX 8

Is 8 angstrom buffer appropriate for my system? In general, how do I know what size of buffer to use relative to the size of a protein? The side of water box after constant pressure equilibration is 60 angstrom.


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Received on Wed Jul 06 2005 - 17:53:01 PDT
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