Dynamically resizing waterbox

From: Nur Aida Abdul Rahim (aida_at_MIT.EDU)
Date: Wed Jul 14 2004 - 14:22:26 CDT

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!


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