请教关于平衡相过程中的six-replica replica exchange simulations问题 - 计算化学公社

In total, one 1 μs extended simulation and two 200 ns six-replica replica exchange simulations (reA and reB) were performed for the apo and holo states (6.8 μs total) using GROMACS 2019 [66]. For the extended and reA simulations, the systems were energy minimized with asteepest descent method until the maximum force on any atom was < 1000 kJ mol-1 nm-1.Atom positions were equilibrated in six steps, during which atom restraints were gradually released. The first two equilibration steps were run for 25 ps with constant temperature (303.15 K) and volume (NVT ensemble), with atime step of 1fs. The next four equilibrations were run in constant temperature (303.15 K) and pressure (1 bar) (NPT ensemble), the third step for 25 ps with 1fstime step and the last three for 100 ps with 2fstime step. The equilibrations used a Berendsen thermostat [67] and aBerendsen semiisotropic barostat [67]. The production simulations were run with constant temperature and pressure (1 bar) using aNose-Hoover thermostat [68,69] and aParrinello-Rahman barostat [70,71]. The protein and lipids were described by the additive all-atom forcefields C36m Protein [72] and C36 lipids [73], respectively, and the water molecules were described with the TIP3P model [64]. The electrostatic interactions were calculated with the fast smooth particle mesh Ewald method with acut off of 12 Å [74,75]. Bonds involving hydrogen atoms were constrained with the LINCS algorithm [76,77]. To improve the sampling, we ran replica exchange simulations [78] using six replicas at closely spaced temperatures (303.15–303.20 K).