(GROMACS) I have a multiple chain , while calculating rmsf , each chain is again starting from residue 1 but i wanted to get a continous graph ,so help me to get a continous rmsf graph or help me in renumbering the .tpr and .xtc file so that i can generate a continous graph .
thanking in advance.
You need to create an index:
$ gmx make_ndx -f md.tpr -o index.ndx
then seprate your residues,
Now do Rmsf analysis by -n index:
gmx rmsf -s md.tpr -f md_noPBC.xtc -n index.ndx -o rmsf.xvg
how to separate residue by index
Group 0 ( System) has 428401 elements
Group 1 ( Protein) has 26944 elements
Group 2 ( Protein-H) has 13564 elements
Group 3 ( C-alpha) has 1708 elements
Group 4 ( Backbone) has 5124 elements
Group 5 ( MainChain) has 6836 elements
Group 6 ( MainChain+Cb) has 8452 elements
Group 7 ( MainChain+H) has 8496 elements
Group 8 ( SideChain) has 18448 elements
Group 9 ( SideChain-H) has 6728 elements
Group 10 ( Prot-Masses) has 26944 elements
Group 11 ( non-Protein) has 401457 elements
Group 12 ( Water) has 401409 elements
Group 13 ( SOL) has 401409 elements
Group 14 ( non-Water) has 26992 elements
Group 15 ( Ion) has 48 elements
Group 16 ( NA) has 48 elements
Group 17 ( Water_and_ions) has 401457 elements
Group 18 (Protein_&_C-alpha) has 1708 elements
i got this output
I am working on tetramer each chain contain 427 residues
thanks in advance
- Badges
- Science topic