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i have used this command for rmsd gmx rms -s em.tpr -f md_0_10_center.xtc -n index.ndx -tu ns -o rmsd_unl1.xvg but i got weird rmsd and rmsf. my protein has two chains. i dont know why i got this error. i m new to simulation. please some one guide me
Have you visualized the trajectory after re-centering the chains to the center of the box? This is most likely due to Chains drifting out of the box. One another thing, -tu: Are you sure, it is ns and not ps? Try re-centering the Chains and compute rmsd and rmsf again.