[gmx-users] Simulation of membrane protein

[Justin A. Lemkul]

James Starlight wrote:
> Dear Justin,
> 
> After 20 iterations I've obtained structure like this 
> http://www.sendspace.com/file/gyyj38
> 
> 
> I suppose that this variat is more closely to correct form :)
> 

I can't access the file, so I don't know.  20 iterations still doesn't sound 
like enough for the tutorial system, unless you shrunk faster than what was 
recommended.

> But during solvation via GenBox I've obtained that error
> 
> One of the box vectors has become shorter than twice the cut-off length 
> or box_yy-|box_zy| or box_zz has become smaller than the cut-off.
> 
> Where I can change that cut-off distance?
> 

There is no reason that your system should be this small to trigger this error. 
  The box dimensions should be on the order of 6 nm.  genbox uses a search 
radius for deleting overlapping molecules.  Perhaps the value you have set in 
vdwradii.dat for C radii is too large for genbox to function properly.  Without 
more detail, I can't suggest anything else.  The procedure in the tutorial 
should work; I've run through it dozens of times.  Please pay careful attention 
to all of the values specified in all of the necessary files and commands.

-Justin

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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