[gmx-users] Re: Adsorption layer of water molecules

[ypca]

The increase of the box volume occur in the beginning of the npt
equilibration. The analysis of pressure was like that:

Pressure nvt = fluctuates between 500 bar
Pressure npt = fluctuates 1 bar
Pressure in production stage = fluctuates 1 bar

Actually, the problem is that water molecules go very far away from the
protein.
These are links to the images of the protein in water, one view close and
another with a smaller zoom. It's like the box has exploded and water has
became free, like no interactions occur between the protein and water.

http://www.dta.ufv.br/arquivos/proteinaway.png
http://www.dta.ufv.br/arquivos/proteinclose.png

Thanks for looking into it!





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