Explicit symplectic integrators of molecular dynamics algorithms for rigid-body molecules in the canonical, isobaric-isothermal, and related ensembles

Abstract

The authors propose explicit symplectic integrators of molecular dynamics (MD) algorithms for rigid-body molecules in the canonical and isobaric-isothermal ensembles. They also present a symplectic algorithm in the constant normal pressure and lateral surface area ensemble and that combined with the Parrinello-Rahman algorithm. Employing the symplectic integrators for MD algorithms, there is a conserved quantity which is close to Hamiltonian. Therefore, they can perform a MD simulation more stably than by conventional nonsymplectic algorithms. They applied this algorithm to a TIP3P pure water system at 300 K and compared the time evolution of the Hamiltonian with those by the nonsymplectic algorithms. They found that the Hamiltonian was conserved well by the symplectic algorithm even for a time step of 4 fs. This time step is longer than typical values of 0.5-2 fs which are used by the conventional nonsymplectic algorithms.

Translational diffusion of water inside hydrophobic carbon micropores studied by neutron spectroscopy and molecular dynamics simulation

“…Each graphene plate comprised 364 carbon sites described atomistically as Lennard-Jones spheres characterized by ǫ cc /k = 28 K and σ cc /k = 3.40 A [36,37]. These plates were immersed into an aqueous fluctuating cubic simulation box to perform isobaricisothermal molecular dynamics at ambient pressure and temperatures in the range 220 ≤ T ≤ 280 K , according to a Nosé-Poincare symplectic integration algorithm [38,39] with a time-step of 2.0 fs, where the aqueous environment consists of 2048 SPC/E water molecules [40]. Some useful additional details about the molecular dynamics can be found in the provided supplemental material document.…”

Dynamics of Thioether Molecular Rotors: Effects of Surface Interactions and Chain Flexibility

“…For each molecule and each of the 5 temperatures used (25, 35, 50, 78, and 100 K), 10 trajectories were obtained. To maintain a constant temperature in the simulations, a Nose-Poincare thermostat 43 with the symplectic integrator for rigid-body MD was utilized. 44 All trajectories were 2.5-5 ns long since a variable time-step approach was used.…”

Protein Simulations by Multibaric–Multithermal Molecular Dynamics Algorithm

“…The time step was taken to be Δt = 0.5 fs for the protein atoms and Δt = 4.0 fs for the water molecules. Because the symplectic rigid-body algorithm was used for the water molecules here, Δt was able to be taken as long as 4.0 fs [31]. Figure 3(a) shows time series of root mean square deviation (RMSD).…”

“…Cutoff distance was r c = 12 Å for both electrostatic and Lennard-Jone potential. The combination [31] of the Nosé-Hoover thermostat [1][2][3], the Andersen barostat [4], and the symplectic quaternion scheme [30,34] was used for the rigid-body water molecules. Reversible multiple time scale molecular dynamics [38] techniques were also applied.…”

“…The temperature was set as T 0 = 600 K and the pressure was set as P 0 = 300 MPa. The MD simulations were performed with the symplectic combination [30,31] of the Nosé-Poincaré thermostat [32,33], the Andersen barostat [4], and the symplectic quaternion scheme [34]. In order to obtain an optimal multibaric-multithermal weight factor W mbt (E, V), two-dimensional versions of both the iterative method [22][23][24] and the Wang-Landau techniques [25], for multicanonical weight-factor determination were employed.…”