Root mean square fluctuation


Root mean square fluctuation

The mean square fluctuation (MSF) is a measure of the deviation between the position of particle i and some reference position.

MSF=frac{1}{T}sum_{t_j=1}^{T}(x_i(t_j) - ilde{x}_i)^2,

where T is the time over which one wants to average, and ilde{x}_i is the reference position of particle i. Typically this reference position will be the time-averaged position of the same particle i, ie. overline{x}_i

Note that where the difference between RMSD and MSF is that with the later the average is taken over time, giving a value for each particle i. With RMSD the average is taken over the particles, giving time specific values.

See also

*Quadratic mean
*Root mean square deviation (bioinformatics)
* Root Mean Square Fluctuation calculated by GROMACS [http://www.gromacs.org/documentation/reference/online/g_rmsf.html]


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