The potential of mean force (PMF) and its RMSD of the association and permeation of vitamin B<sub>12</sub> through BtuB upon coupling of the GF-SA method with umbrella sampling (US).
Tomasz Pieńko
Joanna Trylska
10.1371/journal.pcbi.1008024.s011
https://plos.figshare.com/articles/figure/The_potential_of_mean_force_PMF_and_its_RMSD_of_the_association_and_permeation_of_vitamin_B_sub_12_sub_through_BtuB_upon_coupling_of_the_GF-SA_method_with_umbrella_sampling_US_/12596922
<p>Every 0.2 ns, the RMSD of the PMF was computed taking into account accumulative data. The colors in the legend number each GF-SA-US simulation cycle after which the shown PMFs were computed. This means that the PMFs were calculated based on the data collected from 0 to 1<sup><i>st</i></sup> cycle, from 0 to 2<sup><i>nd</i></sup> cycle, etc., and from 0 to 10<sup>th</sup> cycle.</p> <p>(TIF)</p>
2020-07-01 17:43:18
inner-membrane TonB protein
luminal domain
coli Vitamin B 12
BtuB receptor
TonB-dependent transport system
vitamin B 12
Gaussian force-simulated annealing ...
cobalamin
Vitamin B 12
GF-SA
BtuB extracellular loops