COnfusion on Implimentation of pairdist and rms

GROMACS version: GROMACS/2021.3-foss-2021a
GROMACS modification: Yes/No

Hey There,

I’m reaching out for guidance on generating an RMSD plot using GROMACS for my PhD research. Specifically, I need to analyse a molecule’s insertion into DNA over the entire trajectory. My initial attempt with gmx rms compared the molecule’s trajectory positions to a single reference position of the DNA insertion site, rather than to corresponding frames throughout the trajectory.

Could you advise whether there’s a method to plot RMSD by comparing the positions of the molecule and the DNA insertion site across each frame of the trajectory?

Additionally, I have experimented with gmx pairdist and obtained a promising graph. However, I am uncertain if it reflects the center of mass for both groups. Would adding the -selpos mol_com option calculate the center of mass for both the molecule and the DNA insertion site?

Your prompt assistance would be greatly beneficial as I am approaching the deadline of my doctoral program.

many thanks in advance,