I've done a 50 ns protein-ligand MD simulation. Getting stable RMSD for the first 20 ns, but it increases afterwards, and at some point frame, it's getting very high. My question is, is my md simulation ok? or do I've to increase the time for the simulation until the protein-ligand complex finally converges?
Increase the time for the simulation until the protein-ligand complex finally converges.
The system has obviously undergone major changes, but RMSD cannot tell you where in the system those changes happened. You have to look at the whole structure to know that. That should be the first step in your analysis...
https://m.facebook.com/groups/654236308757812/permalink/1004307280417378/
Hello,
You need to extend the simulation time (atleast 100ns) then only you can confirm about the stability of the protein.
In 50ns trajectory, system equilibrilation artifacts mostly occurs as the system isn't equilibrated fully.
Regards
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