Hello,I’m new in GROMACS. I’m facing a problem with RMSD calculation for protein-ligand complex.After running the code for RMSD,what should I choose for RMSD calculation if I want to create graph like the attached picture between following options-
“Group 0 ( System) has 143213 elements
Group 1 ( Protein) has 9170 elements
Group 2 ( Protein-H) has 4624 elements
Group 3 ( C-alpha) has 581 elements
Group 4 ( Backbone) has 1743 elements
Group 5 ( MainChain) has 2323 elements
Group 6 ( MainChain+Cb) has 2893 elements
Group 7 ( MainChain+H) has 2882 elements
Group 8 ( SideChain) has 6288 elements
Group 9 ( SideChain-H) has 2301 elements
Group 10 ( Prot-Masses) has 9170 elements
Group 11 ( non-Protein) has 134043 elements
Group 12 ( Other) has 72 elements
Group 13 ( LIG) has 58 elements
Group 14 ( SOD) has 14 elements
Group 15 ( Water) has 133971 elements
Group 16 ( SOL) has 133971 elements
Group 17 ( non-Water) has 9242 elements”
If you want to calculate protein rmsd then choose Group 4 (Backbone) twice.For this the command should be like below
Command : gmx rms -s EM.tpr -f [name of md file].xtc -o rmsd-backbone.xvg
4
4
If you want to calculate ligand rmsd then choose Group 13 (LIG) twice. For this the command should be like below
Command : gmx rms -s EM.tpr -f [name of md file].xtc -o rmsd-ligand.xvg
13
13
By running this two command you will get two .xvg file which you can observe in xmgrace.
To open the two .xvg file together in xmgrace run the following command into your terminal
Command: xmgrace rmsd-backbone.xvg rmsd-ligand.xvg
If you want to open it individually then you can give command xmgrace.rmsd-backbone.xvg (it will open the backbone file) or xmgrace.rmsd-ligand.xvg (it will open the ligand file).
If you open the two file together then you will get a graph like below
