RMSD of protein-protein complex

User discussions
1

GROMACS version: 2023
GROMACS modification: No
Here post your question:
Why do I get such straight line

rmsd_fit
rmsd_fit1169×826 40.4 KB

graph after RMSD analysis? How can I solve it?

2

We dont know what you did. providing more information would be helpful, did you applied any restrain and what molecule is this? etc

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3

It is protein-vaccine complex. Yes, I applied Position restraint with ITP file during MD run step. Oh I see! this position restrain could be the reason of this. It restricts the movement of these atoms or groups in simulated system. Do I need to perform the MD run part in this case without applying position restrain?

4

Yes, you need to remove the restrain.