How to sort out the chain numbering issue, each numbered from 1?

GROMACS version:2020
GROMACS modification: Yes
Here post your question

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?

you can visualize the trajectory file to see what happens at 40 ns (for example). It can be that one of your chains is jumping in and out the box.
If it is the case you can post-process the trajectory using gmx trjconv and different workflow (see here for suggest workflow Terminology — GROMACS 2021 documentation or other posts in the forum).

Best regards

1 Like

Hi Alessandra, thank you so much! Yes, it is the periodic boundary condition issue.

After using -pbc nojump, the “jump” disappears!