I have done 15ns MD simulations at 300k temp for a protein finally obtained an average structure from g_rmsf. so please tell me is output average structure is a sampled structure? is there no need of remd or sampling further because I got plateau in RMSD calculation at last?
I have strongly energy minimize by first steepest second by conjugate gradient of my protein after simulation was completed. I have got 81% residues in core region of RC plot by using this energy minimization method. I have also used SPDBv instead of former one method for EM but got 91% core region residues. Which methods should I choose to get the good model? what are the essential criteria for a good model? -- Pawan
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