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 Sara -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists