3.7.1 MD simulation
The MD simulation was performed using GROMACS 5.1.4 on in-house super
computing platform as earlier implementing the GROMACS 53a6 force
field.58 The initial structure was solvated with a
simple point-charge model of SPC water in a box. Na+ions were added to neutralize the negative charges in the system. The
system was then subjected to a steepest descent energy minimization to
give the maximum force below 1000 KJ/mol/nm. After energy minimization,
the position restraint simulation of 2000 steps (2fs each steep) was
implemented under NVT (the constant Number of particles, Volume and
Temperature) and NPT (the constant Number of particles, Pressure and
Temperature) condition. In the end, 50ns MD simulation was conducted on
each ensemble. The root means square deviation (RMSD) and the root mean
square fluctuation (RMSF), which is an important index for evaluating
the protein structure, were calculated using GROMACS rms and rmsf tools.
Time dependent secondary structure was calculated using do_dssp tool.
The Particle Mesh Ewald method was used calculated long-range
electrostatic forces. The neighbor list was determined with the Grid
method. The time step of the simulations was 2 fs, and the coordinates
were saved for analysis every 2 ps. Postprocessing and analysis were
performed using standard GROMACS tools and Visual Molecular Dynamics
(VMD).