I have a gro file from an equilibration run of my protein. When I opened this using VMD, parts of the protein have moved out of the water box. I tried the following command to move the protein back into the water box as follows,
gmx trjconv -f equilibration.gro -s equilibration.tpr -o equilibration_pbc.gro -pbc nojump
However, the new gro file still looks the same as the old one. Am I doing something wrong? Also, does this have anything to do with comm-grps or compressed-x grps/energygrps? I left them empty in the mdp file.
You should make molecules whole before removing jumps.
Thanks! For users who are facing something similar, I found this to be really helpful,
1 - To make broken molecules whole:
gmx trjconv -f output.gro -s system.tpr -o new1.gro -pbc whole – Select the whole system - group 0
2 - Check if atoms jump across the box and put them back into the box:
gmx trjconv -f new1.gro -s system.tpr -o new2.gro -pbc nojump – Select the whole system - group 0
3 - Cluster all the atoms in a specific chosen group, and center the system in the box:
gmx trjconv -f new2.gro -s system.tpr -o new3.gro -pbc cluster -center yes – Select the the solid for the clustering and the centering, then select the system for output.