We have a modelled protein structure (unliganded), about 470 amino acids in length. On running ~70ns production run, we notice the RMSD plot reaching a plateau at ~5A. Is this an acceptable value? Generally, while considering model stability, should we concentrate on the value of RMSD or the plot profile? Energy profiles also look pretty much stable.
Any references would be highly appreciable.
Thanks
Dear Suchetana,
RMSD is pretty general measure and it gives you information rather on "how far from the starting structure current state is" than on stability of a system, or reveal dramatic conformational changes - obviously, there're more possibilities.
The acceptable values are strictly dependent on your system and may vary according to its character, size etc., therefore, it's impossible to point really general rules.
Nevertheless, if a system stabilizes in terms of RMSD plot - as you mentioned - I wouldn't care that much. It may simply mean that your system's initial coordinates were pretty far from equilibrium state in terms of force field of your choice and chosen MD parameters. Moreover, 5A is not that big value in general.
Please note that to follow something like "stability" you should analyze free energy changes rather than potential energy or other structural properties.
Good luck!
Thanks Rafal! Would you be having any publication to support this, as I need to place my case to reviewers strongly.
I have provided few publications that shall support your cause, couple of them from plos one.
Article Homology Modeling of Dopamine D2 and D3 Receptors: Molecular...
Article Comparative Molecular Dynamics Simulations of Mitogen-Activa...
Article Modelling of Thyroid Peroxidase Reveals Insights into Its En...
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