GROMACS version: 2022.3
GROMACS modification: Yes/No
Deal all,
md.mdp (2.6 KB)
I am Anamika Kumari, doing PhD in IIPE, Visakhapatnam. I am working with a dimeric and tetrameric protein system containing one and two ligands, respectively, and I have performed a 100 ns molecular dynamics simulation. After completion of the simulation, I observed that the protein-ligand complex was drifting outside the simulation box during visualization, and therefore attempted to remove periodic boundary condition (PBC) artifacts.
To address this issue, I applied multiple PBC correction options available in GROMACS, including molecule-based reconstruction, jump removal, and centering. Specifically, I tested combinations of -pbc mol, -pbc nojump, -pbc whole, and -center to ensure the integrity and proper positioning of the complex. I also applied PBC corrections using molecule-based and jump-removal options, followed by centering. Specifically, I used the following command:
gmx trjconv -s md_0_100.tpr -f md_0_100.xtc -o md_noPBC.xtc -pbc nojump -center
After applying this correction, the overall protein–ligand complex appeared intact and centered. However, upon visualization, I observed that certain residues appeared to be missing or discontinuous, particularly within the oligomeric protein chains. I have attached md.mdp file and a part of protein where residues disappeared.
I would appreciate guidance on the correct PBC correction workflow for multimeric protein–ligand systems, and advice on how to prevent residue discontinuities while maintaining structural integrity during post-processing and visualization.