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.
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
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.