Hi,
On Tuesday, July 26, 2011, Bruno Rodrigues <bbrodrigues.gmail.com> wrote:
> yeap, but I guess what he meant with "asymetric" box is: well, if I'm
> pulling on z direction, I can choose to have 10A from each border and say,
> 20A from the upper z border, then I'm free to stretch the biological stuff
> and still be within the 10A safe distance and moreover be inside the
> original image, and avoid later work on re-imaging everything to the
> original box.
This is true, but remember that if there is nothing preventing your molecule
from rotating in the box while stretching (and therefore interacting in the
xy plane), you may still need a decent buffer in that plane.
> On NAMD it's pretty easy, because you really design the box, based on the
> basic vectors, like the solid state vectors of the lattice. But how to
> construct such an "elongated z-direction" box on AMBER?
I think you can do something like this in leap:
solvatebox mol TIP3PBOX {x y z}
where x y and z are the relative sizes you would like the x, y and z box
lengths to be. I say relative because in my experience the lengths never
come out to be exactly what you put in (although the ratios stay the same)
so you may have to experiment if you have particular target lengths in mind.
-Dan
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Received on Tue Jul 26 2011 - 13:30:02 PDT
