Dear Community members, I am following the protein-ligand tutorials written by Dr. Justin Lemkul. I have one doubt. After performing a 100 ns simulation of a protein ligand complex, I am recentering and rewrapping coordinates by using the command
gmx trjconv -s md.tpr -f md.xtc -o md_center.xtc -center -pbc mol -ur compact
I also found in the tutorials that for smoother visualization we can use the command
gmx trjconv -s md.tpr -f md_center.xtc -o md_fit.xtc -fit rot+trans
I would like to know whether the rotational and translational fitting is absolutely necessary. What are the specific cases or conditions where performing rot+trans fitting would prove to be helpful? Whether performing rot+trans fitting would yield different results for the analysis and visualization in comparison to the routine recentering and rewrapping procedure?
Thankyou for taking time out for reading my question. Thanks in advance.