[gmx-users] Simulation of membrane protein

Justin A. Lemkul jalemkul at vt.edu
Mon Oct 17 19:05:22 CEST 2011

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 

> 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 A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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