GROMACS modification: Yes
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When I set up the MD, my protein has two chains.
) One chain has residue from 1 to 597, atom from 1 to 9517
) The other chain has residue from 1 to 68, atom from 9518 to 10601
(It is a mistake that I did not number the second chain from 598 onwards)
The MD went all well. When the common analysis is used to analyse the trajectory:
echo 1 1 | gmx trjconv -s md_0_1.tpr -f md_0_1.xtc -o md_0_1_fit-rot_trans.xtc -ur compact -fit rot+trans echo 1 1 | gmx rms -s md_0_1.tpr -f md_0_1_fit-rot_trans.xtc -o rmsd.xvg -tu ns
echo 1 means using the
Protein, i.e. both chains, as the reference. The result shows that, there are occasionally too high RMSD values of more than 3 nm. I think this is because, the software get confused about the residue index from 1 to 68, as those 68 residues can refer to either the first chain or the second chain.
I tried to create an index file, listing the atoms from 1-10601, to run the RMSD, still got the same result of too high RMSD values.
echo a_1-10601 a_1-10601 | gmx rms -s md_0_1.tpr -f md_0_1_fit-rot_trans.xtc -o rmsd_a_1-10601.xvg -tu ns -n index.ndx
If I only index the atoms for one chain, e.g. 1-9517, and use it to run the RMSD, I can get reasonable result.
echo a_1-9517 a_1-9517 | gmx rms -s md_0_1.tpr -f md_0_1_fit-rot_trans.xtc -o rmsd_a_1-9517.xvg -tu ns -n index.ndx
Thus, the current situation is,
) the RMSD for the first chain alone is reasonable
) the RMSD for the second chain alone is reasonable
) the RMSD for the two-chain protein together has high values from time to time.
I also do not think the two chains have dissociated during the MD. As once it is dissociated, it is “impossible” to associate back.
So, is there a way to re-index the residues? Or my interpretation is incorrect?