# RMSD for Protein-Ligand complex

**URL:** <https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974>\
**Category:** User discussions\
**Created:** [August 24, 2024, 1:04pm UTC](https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974 "2024-08-24T13:04:59Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![rhb106](https://avatars.discourse-cdn.com/v4/letter/r/ecd19e/32.png) [@rhb106](https://gromacs.bioexcel.eu/u/rhb106)\
**Post date:** [August 24, 2024, 1:04pm UTC](https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974/1 "2024-08-24T13:04:59Z")

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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”  
 ![Screenshot 2024-08-24 190542](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/e/e3566ac0347dd1f09f1334e8670758e1a1e39c78.png)

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**Author:** ![Sounak\_Biswas](https://avatars.discourse-cdn.com/v4/letter/s/3ec8ea/32.png) [@Sounak\_Biswas](https://gromacs.bioexcel.eu/u/Sounak_Biswas)\
**Post date:** [August 24, 2024, 4:51pm UTC](https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974/2 "2024-08-24T16:51:03Z")

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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

 ![Screenshot from 2024-08-23 01-20-41](https://europe1.discourse-cdn.com/flex017/uploads/bioexcel1/original/2X/a/a752d8556b63dc832b2534ab11925b29efa5eb68.png)

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**Author:** ![Diahdd96](https://avatars.discourse-cdn.com/v4/letter/d/ba9def/32.png) [@Diahdd96](https://gromacs.bioexcel.eu/u/Diahdd96)\
**Post date:** [July 13, 2026, 4:12am UTC](https://gromacs.bioexcel.eu/t/rmsd-for-protein-ligand-complex/9974/3 "2026-07-13T04:12:21Z")

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Hi, may I ask what best way or the difference in analyzing a rmsd? I used to do this : i run two kinds of MD, protein only and protein with ligand, each I calculate the rmsd then i compare both in xmgrace. I see that this is different with what you explained