GROMACS version: 2024.2
GROMACS modification: No
Hi,
I know there is a lot of post related to PBC issues and high RMSD values. I have tried many options, but nothing seems to solve the issue.
I’m getting a surprisingly very high RMSD for my protein-ligand simulation, which looks like this as follows.
When I watched the trajectory it seemed like complex is breaking at several points during the md run.
Plot 1
The recentering steps I have followed,
gmx trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_center.xtc -center -pbc mol -ur compact
Followed by created a new index group for LIG, and calculated the RMSD with a -nopbc flag which gave a plot like this.
Plot 2
Alternatively, I went through the suggestion from other discussions threads, and performed recentering as followed,
gmx trjconv -f md_0_100.xtc -s md_0_100.tpr -o md_whole.xtc -pbc whole
followed by,
gmx trjconv -s md_0_100.tpr -f md_whole.xtc -o md_cluster.xtc -pbc cluster
And finally,
gmx trjconv -s md_0_100.tpr -f md_cluster.xtc -o md_final.xtc -pbc nojump
which gave a plot as follows (no index group created for LIG),
Additional information:
My ligand is Moracin D, it’s uncharged. It had quite high binding energy when docked in autodock vina.
Question:
Am I missing something in my workflow or applying these commands incorrectly? Any guidance would be greatly appreciated.
Thank you!