[gmx-users] box of simulation

Mark Abraham Mark.Abraham at anu.edu.au
Wed Aug 15 14:53:19 CEST 2012

On 15/08/2012 10:27 PM, mohammad agha wrote:
> Dear Mark,
> Unfortunately, my problem about box of simulation has not been solved!
> My command lines are as follow:
> 1- genbox -ci solute.gro -nmol 150 -box 12 12 12 -o solute150.gro
> 2- editconf -f solute150.gro -o solute1501.gro -c -d 1.0 -bt cubic -box 13.6 13.6 13.6 -center 6.8 6.8 6.8
> 3- grompp -f em.mdp -c solute1501.gro -p topol.top -o em1.tpr
> 4- mdrun -v -deffnm em1
> 5- genbox -cp em1.gro -cs cyclohexane.gro -o solutecyc.gro -maxsol 8870
> 6- grompp -f em.mdp -c solutecyc.gro -p topol.top -o em2.tpr
> 7- mdrun -v -deffnm em2
> 8- genion -s em2.tpr -o solutecycion.gro -p topol.top -nname BR- -nn 150
> 9- grompp -f em.mdp -c solutecycion.gro -p topol.top -o em3.tpr
> 10- mdrun -v -deffnm em3
> 11- grompp -f pr.mdp -c em3.gro -p topol.top -o pr.tpr
> 12-  mdrun -v -deffnm pr
> And topology file has been justified with correct numbers for component. After equilibrium (NPT ensemble), size of box change to 12.45*12.45*12.45, but before equilibrium at step 6 had an error, if I had defined size smaller than 13.6*13.6*13.6 and it couldn't place 8870 cyclohexane into the box!!!
> May I ask you to say me where is my problem, Please?

You're solvating 150 randomly placed molecules with cyclohexane using 
genbox. genbox just overlays the coordinates in the two boxes, and 
removes the overlapping solvent molecules. You have so much surface area 
of solute and such a large solvent that you're certain to have lots of 
voids in your solvated system where genbox was unable to fit them around 
each other. Hence the density will be wrong. So you need a more cunning 

g_membed is intended for "solvating" a protein with a membrane, which 
has the same kind of issues you are seeing, so you may be able to adapt 
that for your needs. There are other methods out there, I believe.


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