GROMACS version:
GROMACS modification: No
Hi everyone,
I am working on a docked protein-protein complex to study their interactions leading to oligomerization. Currently, I am facing issues with periodic boundary conditions (PBC) and simulation artifacts. I have run an all-atom MD simulation using the AMBER99 force field for 500 ns in a triclinic PBC box at 310 K.
I have tried my best to resolve PBC-related issues and artifacts using various gmx trjconv commands to center the system and remove jumps. However, I still observe noise in the preprocessed trajectory, especially when analyzing RMSD. I have attached the rmsd.xvg file for reference.
Here are the commands I used:
gmx trjconv -s PPI_md.tpr -f PPI_md.xtc -o whole.xtc -pbc mol
Selected: 1 (Protein)
gmx trjconv -s PPI_md.tpr -f whole.xtc -o centered.xtc -center -pbc mol
Input group: 1 (Protein), Output group: 1 (Protein)
gmx trjconv -s PPI_md.tpr -f centered.xtc -o fitted.xtc -fit rot+trans
Selected: 1 (Protein)
gmx trjconv -s PPI_md.tpr -f fitted.xtc -o final.xtc -pbc mol
Selected: 1 (Protein) for both input and output
Despite these steps, the RMSD plot still shows unusual fluctuations. I’m not sure what I’m missing. Any suggestions or insights would be greatly appreciated.
Thank you in advance!
