Table 1 Jensen-Shannon divergence based on Cα RMSD between α-synuclein ensembles from Martini simulations and atomistic simulations

From: Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution

 

Martini 3

Martini 3 λPP=0.88

A03ws

A99SB-disp

Martini 3

0.0

0.043

0.049

0.065

Martini 3 λPP=0.88

 

0.0

0.039

0.040

A03ws

  

0.0

0.048

A99SB-disp

   

0.0

  1. Comparison of unmodified Martini 3 and Martini 3 λPP = 0.88 simulations of α-synuclein with a 20 μs simulation with the Amber03ws force field and a 73 μs simulation with the Amber99SB-disp force field from Robustelli et al.58. The values shown are the Jensen-Shannon divergence calculated with the DRES approach in Encore56,57 based on dimensionality reduction of the Cα RMSD between structures in the two ensembles. The lower bound is 0, corresponding to two identical ensembles, and the upper bound is ln(2) (~0.69).
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