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Analysis of the evolution of secondary structure as a function of time in the simulation was determined by analysis of the trajectories with GROMACS [24].
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(D ) The angle θ (illustrated in [ A ]) is shown as function of time in the three independent simulations of the 1-ligand EGFR homodimer, for the ligand-free subunit (middle) and for the ligand-bound subunit (right).
(B, C ) Average distance between the centers of the three α-helices at the N-terminus (B ) or the C-terminus (C ) of the coiled coil as a function of time in MD simulations.
The rmsd from the initial structure as a function of time in Figure 5 shows that the simulation had reached a new pseudosteady state.
Figure 22 Number of cells as a function of time for the AMR simulation.
Number of cells as a function of time for the AMR simulation.
The potential energy as a function of time during this simulation and the backbone root-mean square distance (RMSD) relative to this structure during the course of the same simulation is shown in Additional file 6 (A-D).
The Hb course as a function of time (expressed as simulation weeks) and the average Hb in each simulation modality are shown in Figure 1 and Table 1, respectively.
Figure 4b shows the total iron in the cLIP and ferritin species as a function of time for early simulation times.
The course unit of time was the simulation cycle, during which everything in the simulation had one opportunity to update.
The evolution of clusters visited by the two simulations as a function of time is reported in Figure 6, where the RMSD from the starting structure is plotted using a different color for each family.
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