Simulation convergence check.We compared the projections of the free energy landscape for each ontogyration radius(Rg)and the number of hydrogen bonds within the protein of two sets of Replicaexchange molecular dynami...Simulation convergence check.We compared the projections of the free energy landscape for each ontogyration radius(Rg)and the number of hydrogen bonds within the protein of two sets of Replicaexchange molecular dynamics(REMD)[1]simulations of AFGP8,which adopt different initialconformations.The multistate Bennett acceptance ratio(MBAR)[2]method was used to combine dataacross all temperatures to obtain the average thermodynamic properties at each temperature.As shownin Fig.S4,the Rg and number of hydrogen bonds agree well with each other,indicating the two sets ofREMD simulations of AFGP8 have reached certain convergence.The convergent REMD data makesfurther analysis convincing.展开更多
文摘Simulation convergence check.We compared the projections of the free energy landscape for each ontogyration radius(Rg)and the number of hydrogen bonds within the protein of two sets of Replicaexchange molecular dynamics(REMD)[1]simulations of AFGP8,which adopt different initialconformations.The multistate Bennett acceptance ratio(MBAR)[2]method was used to combine dataacross all temperatures to obtain the average thermodynamic properties at each temperature.As shownin Fig.S4,the Rg and number of hydrogen bonds agree well with each other,indicating the two sets ofREMD simulations of AFGP8 have reached certain convergence.The convergent REMD data makesfurther analysis convincing.
