[gmx-users] Genbox question

Justin A. Lemkul jalemkul at vt.edu
Wed May 11 19:59:34 CEST 2011

Fabian Casteblanco wrote:
> Hello,
> I was wondering if someone can help me with a general genbox question.
>  I have been using the command line:
> genbox -ci octanol.gro -nmol 1000 -box 5 5 5 -o prop_1000.gro
> to fill a box with 1000 molecules of octanol.  With the smaller
> n-alcohols, it worked fine but as I started using 1-butanol,
> 1-pentanol, (longer carbon chains) up to octanol, Gromacs sometimes
> ends the command with a 'Killedin-Solvent overlap' line at the very
> end.  Sometimes increasing the box size helped, but for 1-pentanol,
> even 7 7 7 box size didn't work.  Also, do these killed runs take up
> some sort of space.  My memory space decreases a little bit even on
> failed runs.

Generating random boxes in this way requires lots of memory and is prone to 
failure.  A useful strategy is to overestimate the size of the box so that 
genbox doesn't have to do too many iterations to place all of the molecules, 
then run a nice, long equilibration to get the box vectors (and therefore 
density, etc) correct.



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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