RMSD & RMSF
To analyze the structural stability of each of the systems throughout
the simulation, we performed RMSD and RMSF calculations. The RMSD values
were calculated for the protein backbone atoms (Figure 1 A ).
Each of the systems attained equilibrium within the first 10
nanoseconds, and the RMSD values of all systems showed deviations within
the range of 5.8 to 6 nm and remained within the range throughout the
trajectory. Tau_plane is relatively stable throughout the simulation,
while Tau_glyc is showing minor fluctuations, within the 0.1 nm range.
Tau_phous shows fluctuations from 800 to 900 ns. The analysis shows
that each of the systems tends to remain stable throughout the
trajectory without any major structural deformations and is converging.