So I have completed production MD for my Protein-Ligand System. My question is regarding gmx_rms RMSD calculation steps.
The tutorial on MD Tutorials suggest that if I am trying to calculate RMSD for my LIGAND, I should choose BACKBONE for the least square fitting step and LIGAND for RMSD step. I have 2 questions:
(1) the silly question : if I choose BACKBONE for the least square fitting step, and LIGAND for RMSD step, will the RMSD be calculated by comparing position of LIGAND in the trajectory compared the the reference position of the LIGAND, right? Whatever (BACKBONE/PROTEIN/LIGAND) I choose for least square fitting step, the RMSD is always calculated by comparing value of X in trajectory vs value of X in reference, right? The tutorial states “By doing so, the overall rotation and translation of the protein is removed via fitting and the RMSD reported is how much the JZ4 (LIGAND) position has varied relative to the protein” - this confused me, isn’t RMSD telling position of JZ4 compared to its position in reference?
(2) why isn’t it more apt to choose LIGAND in the least square fitting step too in addition to choosing LIGAND in the RMSD step.
(3) As I understand, the least square fit works on the trajectory file and then aligns the least square fitted structure to the reference structure. Am I getting this correctly.
GROMACS modification: Yes/No
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