How to get a continous rmsf graph for mutiple chains?

User discussions
1

Hi all.

I have just finished my first MD.
Then I did rmsf analysis as follows
$ gmx rmsf -s md_0_10.tpr -f md_fit_0_10.xtc -o rmsf.xvg -oq rmsf.pdb -res -b 5000
Then I typed ‘1 (Protein)’

The graph of ‘rmsf.xvg’ is as follows.

스크린샷, 2021-07-13 22-43-31
스크린샷, 2021-07-13 22-43-311920×1080 143 KB

My protein complex has 4 chains and it shows each chain starts from its 1st residue.
But, I hope to get a continous graph.

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
Protein_chain_C 1
Protein_chain_D 1
SOL 12116
NA 17

Is there any way to do that after MD, or should I renumber pdb file and do MD again?

Any advice would be greatly appreciated.
Thanks in advance.

Regards,
Suhyeok.

2

Analyze the chains separately using index groups.

3

Umm that’s a way!

It seems like that I should renumber to get continuous rmsf.

Anyway, thanks to the reply.