[gmx-users] sphere around a protein

Justin A. Lemkul jalemkul at vt.edu
Mon May 9 12:21:22 CEST 2011

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 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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