Re: [AMBER] Building a slab between two vacuums?

From: Bill Ross <ross.cgl.ucsf.EDU>
Date: Thu, 10 Jun 2010 09:57:14 -0700

> After having equilibrated a system (cube) I would like to place this
> between to empty spaces (vacuum) and follow the equilibration process
> between the two "phases".

So you want only 2 opposite of the 6 sides to have the empty space adjacent.

> I thought you could change the .rst box coordinates and it worked
> quite well, however, then you only get liquid in one phase and empty
> space in the other.

Not sure what you mean - expanding the box uniformly would give empty
space on 3 sides, none opposite.

> Is there a way to expand the box in the form of empty space on both
> sides of the already equilibrated cube?

Just 2 sides opposite? You could expand the box by a factor of 3 in
one dimension, then write a script to shift that dimension's coords
by a factor of one to put it in the middle. In 2D you'd have:



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Received on Thu Jun 10 2010 - 10:00:08 PDT
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