[gmx-users] Genbox question

[Justin A. Lemkul]

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

-- 
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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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