How to start an MD simulation

Edit the README provided by CHARMM-GUI

Monitoring the progress

• to check the progress

  ` gmx check -f step6.6_equilibration.xtc `

• to extract the trajectory as a PDB file:

  ` gmx trjconv -s md.tpr -f md.xtc -o traj_fixed.pdb -pbc mol -center `

  ` -sep` nagrywa każdą klatkę w odrębnym pliku .pdb