[gmx-users] Ion positioning 2

[Anton Feenstra]

Lieven Buts wrote:
> 
>   I tried my genion run again without
> using the "-bt dodecahedron" option for
> editconf. Now the ions are all around the
> protein (<http://ultr.vub.ac.be/~lieven/ions2.png>),
> so the problem would seem to have something to do
> with the box shape.

Is this perhaps only an apparent problem, meaning that due to the
periodic boundaries, the ions are actually near the protein, but
only appear to be 'far away' because they happen to end up at the
other end of the box? To assess this, you should keep in mind that
the water box using '-bt dode' is also brick-shaped, but that the
stacking of the brick determines that actual box shape, i.e. the
bricks are stacked with a shift rather than directly on top of each
other. You can try:

# trjconv -f conf.gro -s conf.gro -ur compact -pbc inbox -o compact.gro

to convert to a 'compact' representation of your box, in which the
water is no longer 'brick-shaped', but the actual dodecahedral shape
is visible...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
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| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
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