[gmx-users] sphere around a protein

[Justin A. Lemkul]

shivangi nangia wrote:
> Hi Justin,
> 
> I used 15 nm cubic box and 6 nm shell.
> I again tried to insert only 1 histidine molecule in the sphere. I get 
> the same error
> 
> Fatal 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.
> 
> 

Please provide the exact command that gives the error.  I cannot reproduce this 
using a shell value less than half a box vector.  You may also want to try 
starting from a clean directory - get rid of old files and intermediates so 
you're sure you're using the right files.

-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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