Removing Outlier Residues in RMSD and RMSF Calculations - GROMACS

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GROMACS version: 2023
GROMACS modification: Yes/No
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Hello everyone,

I am currently analyzing molecular dynamics simulations involving a ligand and protein using GROMACS 2023. I prepared my system using CHARMM-GUI, but I encountered an issue where some residues of the protein were out of the solvation box before and during the simulation. As a result, these residues show unusually high RMSD and RMSF values.

I would like to exclude these outlier residues from my RMSD and RMSF calculations to obtain more accurate results for the remaining part of the protein. Could anyone guide me on how to exclude specific residues from these calculations in GROMACS?

Thank you in advance for your help!

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The fact that something moves out of the periodic box is not a problem in itself, but make sure that those residues do not end up close enough to interact with the rest of the protein across the periodic boundary. You may need a larger box to avoid self interaction effects.

You can use an index file (the -n option) to specify which atoms you want to include in the analysis. gmx make_ndx and gmx select can be useful to create index files.