Dear Gmx Users, I know that this problem has been discussed may times but I cannot find the solution to get rid of pbc in my system: protein and ligand. I followed the workflow:
1. First make your molecules whole if you want them whole trjconv -f md.trr -s md.tpr -pbc whole -ur compact -o mdwhole.xtc 2. Cluster your molecules/particles if you want them clustered 3. Extract the first frame from the trajectory as reference for removing jumps if you want to remove jumps. trjconv -f mdwhole.xtc -s md.tpr -dump 0 -o 1stframe.pdb 4. Remove jumps if you want to have them removed using the first frame trjconv -f mdwhole.xtc -s 1stframe.pdb -pbc nojump -o mdwholeNOjump.xtc 5. Center your system using some criterion. Doing so shifts the system, so don't use trjconv -pbc nojump after this step. trjconv -f mdwholeNOjump.xtc -center -o mdwholeNOjumpCENTER.xtc 6. Put everything in some box. trjconv -f mdwholeNOjumpCENTER.xtc -box 6 6 6 -o mdwholeNOjumpCENTERbox.xtc 7. Fit if desired and don't use any PBC related option afterwards. trjconv -f mdwholeNOjumpCENTERbox.xtc -s 1stframe.pdb -fit rot+trans -o mdfinal.xtc I used SYSTEM everywhere as output orinput. However, my ligand is still jumping like a fly around the stable protein. Do you have any suggestions? Steven
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