GROMACS version: 2021.2
GROMACS modification: Yes/No
I simulated a protein/ligand complex for 200ns. I centred it around the ligand. However, during the middle of simulation ligands moves two far from the protein. As if it ligand does not bind to the protein at all. However after few ns it again comes to protein at different site. Few snapshots are shown below. My question is it centerling issue? or is it how the ligands binds to protein?
I use following commands for centering.
gmx trjconv -s step4.0_minimization.tpr -f output.xtc -o outputwhole.xtc -pbc whole -dt 10
gmx trjconv -s step4.0_minimization.tpr -f outputwhole.xtc -o outputcluster.xtc -pbc cluster -dt 10
gmx trjconv -s step4.0_minimization.tpr -f outputcluster.xtc -o outputbox.xtc -pbc mol -center -dt 10
I think you are on the right track. You definitely need the reference coordinate file ("-s"). Have you tried “-pbc nojump”?
gmx trjconv -f md_1f_1.xtc -s em_1.gro -n hb_5.ndx -pbc nojump -o tmp_1.xtc
That worked for me with a similar system.
Thank you for your suggestion.
I tried -pbc jump as you sugested. But it did not help.
Presumably you mean “nojump”. What did happen?
Is there a problem with remapping the periodic boundaries in trjconv, or is this ligand simply not bound to the protein? Looking at your 3rd image it looks like maybe the latter. If you look at the raw trajectory in VMD you should be able to tell the difference.
Yes i mean “nojump”. Sorry for typo.
Did you look at the trajectory in VMD? What did you see?
@veerubiotech post an image with PBC box.