MD simulations
All MD simulations were carried out with Amber ff14SB force field by
using the PMEMD module of Amber 18.20 The Particle
Mesh Ewald method was used and nonbonded interactions were calculated
within the cutoff value of 10 Å. Each structure was relaxed through
energy-minimization with 4000 steps steepest descent followed by 1000
steps conjugate gradient. The minimized structure was then heated by
varying the temperature linearly from 0 to 300K in the NVT ensemble and
then subjected to the 10 ns production run under the NPT ensemble. The
SHAKE algorithm was used to constrain the bond length of hydrogen atoms.
A time step of 2 fs was used and the Langevin Thermostat with a
collision frequency of 5 per ps was employed to control the temperature.