[gmx-users] spherical box

[Anton Feenstra]

s8026264 wrote:
> I want to consider unfolding a small protein .
> there are some limitations for a completely unfolding of the peptide,
> if dimention of my box isn't comparable with dimention of the extended 
> protein.
> 
> And if I select a big box , I will have more water molecules and so my time of 
> simulation will be more .
> 
> And so I think that it is suitable that use a sherical shell water . 

But, your sphere of water should be large enough to hold the unfolded protein,
and the same goes for a (periodic) box. I don't see that you would gain much,
unless you create a layer of water around your protein, and extend that layer
as the protein unfolds.

Have you already considered the difference between a cubic and a dodecahedral
box? Going from cubic to dodecahedron already saves you >20% water at a given
distance between protein and box-edge.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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