AMBER Archive (2005)

Subject: Re: AMBER: box size in explicit water

From: David A. Case (case_at_scripps.edu)
Date: Wed Jul 06 2005 - 12:30:59 CDT

On Wed, Jul 06, 2005, Lwin, ThuZar wrote:
>
> solvateOct protein TIP3PBOX 8
>
> Is 8 angstrom buffer appropriate for my system?

8 Ang. is probably a minimum for a realistic simulation. It depends to a
large extent on what you plan to do with the results: how much you are looking
for qualitative behavior vs. quantiative analysis. I generally use 12-15
Ang. as a buffer, but there is nothing magical about such a value. It is
probably the case that even larger cells would be required to obtained results
that were "converged" in terms of cell size.

....hope this helps....dac
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