AMBER Archive (2005)

Subject: AMBER: box size in explicit water

From: Lwin, ThuZar (ThuZar.Lwin_at_stjude.org)
Date: Wed Jul 06 2005 - 11:39:47 CDT

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.

Thanks,
ThuZar

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