GROMACS version:2023.3
GROMACS modification: Yes/No
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We are completed MD simulation of protein-ligand complex. After the MD simulation results we observed bumps in RMSD of protein_lig complex plot but protein is normal. The bumps are good or bad for research or publishing? Can you suggest and am new for MD Simulations.
Did you account for the periodic boundary conditions (example of how to do it is in this tutorial: Lysozyme in Water)? If you have and it’s still resulting in unexpected bumps, try visualizing the trajectory with software like VMD to see if you can identify what’s going on
Thankyou for your response Karis. We are visualizing the Coordination file (solv.gro) and we are identify protein is not completely dissolved in solvation part. It is a reason for bumps in RMSD ? please solve this problem.
Try visualizing the molecule at the time points where the jumps occur (you can use gmx trjconv to extract .gro files at specific time points of a trajectory using -dump) and compare to other points to see what might have gone wrong.
In that documentation, you will also find alternative methods to deal with pbc if -pbc mol doesn’t seem to be working (sometimes I’ve found -pbc nojump works when -pbc mol doesn’t)
Thankyou karis. Is it problem protein is out of PBC and its effect MD simulation results?
As long as the box is large enough that the molecule can’t interact with it’s periodic image, pbc won’t affect the actual simulation (going off Lysozyme in Water, as long as there’s at least 2 nm between the molecule and it’s periodic image, so based off the pictures you sent, you should be fine)
Thankyou Karis.am using the option gmx_latest trjconv -s md_0_10.tpr -f md_0_10.xtc -o md_0_10_new_center.xtc -center -pbc nojump . again generate the center.xtc file using the nojump option. based on this file after am get RMSD between protein and protein_lig like this. Is it wrong?
Should be fine
Thankyou Karis. both protein and protein_lig peaks are similar so can we state that complex is stable as protein?
That RMSD levels off like that does indicate stability, though I’m not familiar enough with your study to provide definitive conclusions beyond what’s already described in this tutorial Lysozyme in Water.
For further guidance on analyzing protein-ligand interactions, you can refer to this as well Protein-Ligand Complex
Thank you karis
