[gmx-users] genbox

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 23 14:13:03 CET 2012

Gavin Melaugh wrote:
> Hi all
> I have a system of 40 solute molecules in a solvent of 480 crown ether
> molecules. I am not trying to insert 100 methane molecules into this
> relaxed and well equilibrated structure using genbox.
> There are clearly visible cavities in the fluid but genbox only alllows
> the insertion of 8 methane molecules. How can I circumvent this problem ?
> The command I use is
> genbox -cp test.gro -ci methane.gro -nmol 100 -try 5 -p combined.top
> where combined.top includes all three itp files, and test.gro is the
> initial solute and solvent configuration.

You might try reducing the value used for -vdwd in genbox, or otherwise 
shrinking the vdW radii in vdwradii.dat, but be warned that if you have to 
finesse the system too much, likely any resulting simulation will be extremely 
temperamental, if you can even get it to run.



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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