On Tue, Aug 24, 2010, colvin wrote:
> 1. Is there any rule or guide in setting the distance value for
> solvateBox?
In principle, the bigger the box, the smaller will be the periodic artifacts.
For "garden-variety" globular, soluble proteins in water, I often use 12 Ang.
as the buffer. But this is not based on any systematic study. You seem to
have a protein-membrane system, but I don't know if it has any two-dimensional
periodicity along the membrane plane or not.
One general suggestion is to find a paper that has done simulations like the
ones you are considering, and use their setup as a starting point. Better,
do a more thorough literature search as see what the current state of the art
is.
....dac
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Received on Tue Aug 24 2010 - 10:00:05 PDT
