[gmx-users] Genbox question

Fabian Casteblanco fabian.casteblanco at gmail.com
Wed May 11 19:56:30 CEST 2011


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.


Best regards,

Fabian F. Casteblanco
Rutgers University --
Chemical Engineering PhD Student
C: +908 917 0723
E:  fabian.casteblanco at gmail.com

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