AMBER Archive (2009)

Subject: Re: [AMBER] Simulating transmembrane protein.

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Mon Oct 12 2009 - 17:37:50 CDT

I don't have any references for such a simulation. One problem
with the limitations I pointed out is that, while a memebrane
itself should be able to wrap in, say, the faces of the box on
the x,y axes, the z axis will wrap the interior of the cell
directly into the exterior. It is a common question here of
whether we could restrict periodicity to two dimensions just
for this reason. So far it looks like the answer is no; not sure
to what extent it's due to physics or available programming time.

Bill

> Thanks for the suggestion. I will try it. Are there any published examples
> of such a simulation? Thanks.
> Jaya.
> On 10/12/09, Bill Ross <ross_at_cgl.ucsf.edu> wrote:
>
> The whole system to be simulated needs to be in one box. You can
> mix solvents in a box. The box is periodic in 3 dimensions.

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