In vacuo 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

editconf -f out.gro -o cmk_ctr.gro -center 3.89025 3.89025 3.89025

steepest descents (1000 steps)

grompp -f st.mdp -c cmk_ctr.gro -p cmk.top -o cmk_em.tpr

mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_vacuum.pdb -g em.log -e em.edr &

Steepest Descents:
   Tolerance (Fmax)   =  1.00000e+03
   Number of steps    =         1000

writing lowest energy coordinates.

Steepest Descents converged to Fmax < 1000 in 5 steps
Potential Energy  = -4.9777656e+03
Maximum force     =  5.3928821e+02 on atom 682
Norm of force     =  1.3912250e+02


conjugated gradient (3000 steps)
grompp -f con.mdp -c cmk_ctr.gro -p cmk.top -o cmk_em.tpr

mdrun -s cmk_em.tpr -o cmk_em.trr -c cmk_EM_vacuum.pdb -g em.log -e em.edr &

Polak-Ribiere Conjugate Gradients:
   Tolerance (Fmax)   =  1.00000e+02
   Number of steps    =         3000
   F-max             =  2.80126e+04 on atom 1512
   F-Norm            =  7.57882e+03


writing lowest energy coordinates.

Back Off! I just backed up cmk_EM_vacuum.pdb to ./#cmk_EM_vacuum.pdb.1#

Polak-Ribiere Conjugate Gradients converged to Fmax < 100 in 68 steps
Potential Energy  = -4.9642773e+03
Maximum force     =  9.7731384e+01 on atom 1636
Norm of force     =  2.3101681e+01