ion wet energy minimisation pdb2gmx -f cmk.pdb -o cmk.gro -p cmk.top -ignh use Gromos 96.1 (43A2) 1 editconf -bt cubic -f cmk.gro -d 1.0 7.78050 7.78050 7.78050 editconf -f out.gro -o cmk_ctr.gro -center 3.89025 3.89025 3.89025 genbox -cp cmk_ctr.gro -cs spc216.gro -o cmk-b4em.gro -p cmk.top Output configuration contains 46207 atoms in 14923 residues Volume : 471.002 (nm^3) Density : 1045.51 (g/l) Number of SOL molecules: 14693 grompp -f em.mdp -c cmk-b4em.gro -p cmk.top -o cmk_em.tpr NOTE 1 [file cmk.top, line 13399]: System has non-zero total charge: -5.999998e+00 genion -s cmk_em.tpr -o cmk_ion.gro -pname NA+ -np 6 -g cmk_ion.log Select a group: 12 Steepest descents (1000 steps) I must run it again grompp -f em.mdp -c cmk_ion.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_ionwet.pdb -g em.log -e em.edr & Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 1000 ruben@rubennb:~/Desktop/EM_latest/Rv1712_ionwet$ ps PID TTY TIME CMD 1844 pts/0 00:00:00 bash 2506 pts/0 00:04:03 mdrun 2531 pts/0 00:00:00 ps ruben@rubennb:~/Desktop/EM_latest/Rv1712_ionwet$ writing lowest energy coordinates. Steepest Descents converged to Fmax < 1000 in 696 steps Potential Energy = -7.9864450e+05 Maximum force = 9.1239026e+02 on atom 109 Norm of force = 2.3338303e+01 Conjugated gradient (3000 steps) I must run it again grompp -f con.mdp -c cmk_ion.gro -p cmk.top -o cmk_em.tpr mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_ionwet.pdb -g em.log -e em.edr & Polak-Ribiere Conjugate Gradients: Tolerance (Fmax) = 1.00000e+03 Number of steps = 3000 F-max = 7.62182e+05 on atom 1815 F-Norm = 5.25147e+03 writing lowest energy coordinates. Back Off! I just backed up cmk_EM_ionwet.pdb to ./#cmk_EM_ionwet.pdb.1# Polak-Ribiere Conjugate Gradients converged to Fmax < 1000 in 32 steps Potential Energy = -7.4641175e+05 Maximum force = 8.9718903e+02 on atom 1817 Norm of force = 7.3749023e+01