[gmx-users] Is it reasonable to get a bad Ramachandran plot after MD?

[Kevin C Chan]

Dear Users,

As the title states, I am wondering the validity behind the outliers appear in a Ramachandran plot of structure after MD. I only have little data on this, but for a 10,000-atom protein, portion of outlier can increase from 0.7% to 5.0%. Is this explainable? Or it simply means my force-field does not care about the dihedral angles but still accurate enough to predict protein dynamics? 

Thanks in advance,

Kevin
PhD Candidate
Department of Physics and Material Science
City University of Hong Kong
ukevi at gmx.hk