How to calculate Pairwise RMSD between two trajectories using `gmx rms`

User discussions
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GROMACS version: 2023.3
GROMACS modification: No
The gmx rms documentation mentions the -f2 option for calculating RMSD between two trajectories with different ligands. After extracting CA atoms from the receptor and creating traj files and a tpr file for them, the RMSD calculation was performed using the command: gmx rms -s receptor_backbone.gro -f ./receptor_backbone_1.xtc -f2 ./receptor_backbone_2.xtc -m pari_rmsd.xpm -tu ns.

However, two questions arise:

  1. In the docs, it says: With -f2 , the ‘other structures’ are taken from a second trajectory, this generates a comparison matrix of one trajectory versus the other. So, does the matrix value[i, j] in the result represent the RMSD of pose_i in traj1 and pose_j in traj2 with alignment as per the documentation?

  2. The diagonal line in the matrix plot shows dark, indicating zero RMSD values at the same times in both trajectories, which seems odd for different ligands. Is there a mistake in the process?

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pari_rmsd
pari_rmsd1920×1440 124 KB