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I am beginner to Gromacs,
I want to calculate RMSD analysis for Protein-ligand complex, Which is compare to Apo protein RMSD.
For complex RMSD, Which group have to Select?
Backbone or to create index file for protein ligand complex.
What group should i select for complex RMSD ?
Can you give your valuable suggestions.
Thanks in advance
You need to compare the same atoms between the two systems to have anything meaningful. If you compute the RMSD of the protein of the apo system and the protein+ligand in the complex, you’re comparing apples and oranges. RMSD is an extrinsic property so if you use more atoms for the calculation, the value can simply increase as a result of having more atoms that are moving around.