From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Fri Nov 04 2005 - 14:29:36 CST
santanu chatterjee wrote:
> is there any way of deciding what size of water box
> (i.e., how many water molecules) should be used to
> solvate any protein? In NAMD tutorial, Ubiquitin is
> solvated using 5 AA water box in each side of the
> molecule. Ubiquitin is of size nearly 600 atoms. Is
> that sufficient for any molecule of similar size?
I'd consider that horribly insufficient. See Hunenberger & McCammon's
1999 paper in Biophysical Chemistry 78(1-2):69-88 for a relevant
discussion. The NAMD tutorials are designed with an eye to feasibility
for low-end systems for demonstration purposes, not scientific rigour.
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