Re: Dynamically resizing waterbox

From: Edward Patrick Obrien (
Date: Wed Jul 14 2004 - 15:01:00 CDT

Hi Aida,

The closest thing I can think of is a paper by Schulten (?), he used a
water sphere and pulled... as the protein stretched the sphere naturally
contorted and became more oblate and solvated the protein as much as
possible. Although, fully stretched I think the protein was not solvated
in some regions. I don't know how you would do such a thing with periodic
boundary conditions.

I don't have the reference, you'll have to search.

Hope that helps,

On Wed, 14 Jul 2004, Nur Aida Abdul Rahim wrote:

> Hi all,
> I'm wondering if it's at all possible to have a dynamically changing waterbox?
> I'd like to unravel my protein but the end-to-end distance is so large such
> that it's computationally virtually impossible to have a waterbox big enough to
> unravel the protein in (>150,000 atoms) with my current computing resources.
> I was thinking of starting with a waterbox ~200angstrom long in the direction of
> unraveling. And as the protein unravels and slants towards the direction of
> unraveling (from a vertical position say) I could remove water molecules on the
> 'top' and 'bottom' of the box and add some on the 'end' of the box.
> Would there be a way of making this realistic at all? Any
> help/suggestions/comments would be appreciated. Thanks!
> Aida

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