[gmx-users] Genbox question

Justin A. Lemkul jalemkul at vt.edu
Wed May 11 20:00:49 CEST 2011

Justin A. Lemkul wrote:
> 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.

A more reliable method is probably genconf:

genconf -f molecule.gro -nbox 10 10 10 -o box.gro

You'll get 1000 molecules every time and the box size should be sensible.  Then 
proceed with equilibration.



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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