Grouping DNA and protein for RMSD calculations

User discussions
1

GROMACS version: 20202
GROMACS modification: No

I would like to perform RMSD calculations for protein-DNA complex in my simulation in order to check the stability of the protein-DNA complex.

How do I group both DNA and protein into one group so that I can perform RMSD analysis using make_ndx.

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How do I proceed with this?

Thank you in advance

2

Hi,

If you want to compute the RMSD of the CA and/or backbone atoms of the protein (only) interacting with the DNA use 3 ou 4.