Research Article

Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations

Figure 1

RMSD as a function of time for trajectory1 (10 ns). Black curve: RMSD between first configuration and all successive ones. Blue curve: for a given configuration ( 𝑡 𝑗 ) , RMSD to each of the other configurations of the same trajectory was computed and averaged, yielding R M S D ( 𝑡 𝑗 ) . That value of 𝑡 𝑗 for which R M S D ( 𝑡 𝑗 ) is maximum is then adopted as a reference ( 𝑡 1 ) to plot RMSD values of the whole trajectory. Red curve: as blue curve, but for minimum R M S D ( 𝑡 𝑗 ) . Note that the RMSD between the reference configuration and itself is zero by definition.
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