[gmx-users] spherical box
feenstra at chem.vu.nl
Tue Jun 10 08:59:07 CEST 2003
> 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
> 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.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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