[gmx-users] shell again

[K.A. Feenstra]

Dmitry Kovalsky wrote:
> 
> Dear David
> 
> I'm sorry if I didn't express correctly myself.
> 
> I'm following an ordinary way.
> When I construct my system, I first create a box for a protein with editconf
> programm.  After I solvate the protein with shell option in genbox (this
> generates few water molecules around the protein) and drope again resulted
> system into genbox to generate all others water molecules in order to fill
> out the box. After this all I remove from final.gro file all waters that were
> generated with first genbox run.

So, you create a 'free space' in between the protein and your water?
Why whould you want that? It can lead to strange things as soon as the
water is free to move, it will 'rush into' the protein, and could
disturb the protein conformation (by my guess, to the point where it
could de-nature!). This would explain why you see a (large) deviation
for the 0.3 nm removed shell, there is a larger 'cavity' between protein
and water which leads to larger impact velocity when the water hits
the protein. Remember that the Lennard-Jones potential has a minimum
at short distance and is attractive at larger distances, so it will
'condense' molecules with empty space inbetween.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Vrije Universiteit Amsterdam |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "If You See Me Getting High, Knock Me Down"               |
|        | (Red Hot Chili Peppers)                                   |
|________|___________________________________________________________|