[gmx-users] Issue with genbox

Justin Lemkul jalemkul at vt.edu
Tue Sep 18 15:27:07 CEST 2012

On 9/18/12 9:21 AM, Bharath K. Srikanth wrote:
> Hi all
> While attempting to simulate the self assembly of a course-grained DSPC
> lipids, I ran into a problem using the genbox command.
> I first used genbox to create a box of 32 DSPC lipids, of dimensions 20 x
> 20 x 20 nm^3. The command used was
> genbox -ci dspc_single.gro -nmol 32 -box 20 20 20 -try 500 -o 32lipids.gro
> This gave me 32 lipids in a random configuration, as expected. I also ran
> en energy minimization on this configuration, with no problems (the file
> 32minimised.gro contained the coordinates after minimisation).
> However, when I tried solvating the box with course-grained water
> molecules using genbox, the added water molecules were formed in a small
> box, at the corner of the lipid box region, and not interspersed with the
> lipid molecules. The command I used was
> genbox -cp 32minimised.gro -cs water.gro -o lipidsandwater.gro -maxsol 192
> -vdwd 0.21
> What could the problem be?

You have a 20-nm cubic box (huge) and you're telling genbox to add only a 
maximum of 192 water molecules.  Given the constraints imposed, you should only 
expect to see a small fraction of your box solvated.  Remove -maxsol and try again.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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