[gmx-users] box of simulation

mohammad agha mra_bu at yahoo.com
Wed Aug 15 12:03:35 CEST 2012

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? 

Best Regards

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