Dear Justin Please check my commands, Are these correct, step by step?
If these are correct then i will start my simulation with longer time, 1- pdb2gmx -f mixture.pdb -o mix -p mix 2- editconf -f mix.gro -o mix2.pdb ; for obtain a clean .pdb for obtaining clean .gro and clean .top 3- pdb2gmx -f mix2.pdb -o mix2.gro -p mix2.top STEP 1 : EM 5- grompp -f minim.mdp -c mix2.gro -p mix2.top -o em.tpr 6- mdrun -v -deffnm em STEP 2 : NVT EQUILIBRATION 7- editconf -f em.gro -o em.pdb ; to earn em.gro and em.top for next NPT EM 8- pdb2gmx -f em.pdb -o nvt -p nvt 9- grompp -f nvt.mdp -c nvt.gro -p nvt.top -o nvt.tpr 10- mdrun -v -deffnm nvt 11- g_energy -f nvt.edr 12- xmgrace energy.xvg Sincerely -- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users * 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
