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The root-mean-square fluctuation (RMSF) calculations
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The RMSF of apo and holo systems were calculated using the ’gmx rmsf’ module of GROMACS (Abraham et al., 2015) and with the following equation:
where simulation time over which one wants to average, and coordinates of backbone atom Xi at time n were denoted by N, and Xi(n), respectively. In this way, the fluctuation pattern of each amino acid was calculated and compared to point out regions where substantial differences were observed.
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