From: Richard Law (rlaw_at_llnl.gov)
Date: Fri Sep 14 2007 - 16:00:08 CDT
The "rule of thumb" that I use is half the width of the protein on either
side. But there's really no good answer to this question. So 100x120x140
(but maybe z could be a lot smaller - more like the "standard" 10A either
I always thought about it in terms of the lipid providing very little charge
screening (relative to water) (thinking about it as if there was an
effective dielectric). So if x and y aren't larger than your cut-off or
large enough to allow the PME calculations to decay to a small number, then
the protein would "see" itself. As many membrane proteins exist in rafts
next to multiple copies of themselves, maybe that would be okay anyway!
Hence why there's really no good answer to this question.
Getting good equilibration, surface tension, lipid density, etc, will
require more rather than less lipid, though.
I hope this helps.
On 9/14/07, youbin tu <youbint_at_gmail.com> wrote:
> Hi all:
> We want to simulate a protein in the membrane. Assume the protien
> is 50X60X70 Angstrom (LengthXWidthXDepth), what size of membrane
> should we use?
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