nanoribbonsphononsthermalconductivityThe thermal conductivity of graphene nanoribbons (GNRs) has been investigated using equilibrium molecular dynamics (EMD) simulation based on Green-Kubo (GK) method to compare two interatomic potentials namely optimized Tersoff and 2nd generation Reactive Empirical Bond Order...
(1.College of Science,National University of Defense Technology,Changsha,410073,Hunan,China;2.College of Op-toelectric Science and Engineering,National University of Defense Technology,Changsha,410073,Hunan,China)Abstract:Equilibrium MD simulation is amethod to investigate the evolution of an initial ...
Second, the simulation must be sufficiently long such that bulk phases can nucleate, which is not easy to capture in an MD simulation because of the longer time scales associated with diffusion. For the time and length scales required to study the thermodynamics of nanostructured states, a ...
For better sampling, 8 independent non-equilibrium MD simulation trajectories were conducted for each inhibitor-CHK1 complex starting with the same initial crystal structure but different random velocities. The cantilever spring constant was k = 600 kJ/mol/nm2, and pulling speed was v = 0.005 nm...
specific protein regions, to large-scale domain rearrangements. Quantitatively, BioEmu samples protein conformations with relative free energy errors around 1 kcal/mol, as validated against millisecond-timescale MD simulation and experimentally-measured protein stabilities. By si...
Left: for the RBD protein, MD simulation reveals four highly populated regions in the 2D space spanned by TICA coordinates. DiG-generated structures are mapped to this 2D space (shown as orange dots), with a distribution reflected by the colour intensity. Under the distribution plot, structures...
the degree of deviation depends on the simulation time, converging at the lowest temperatures under study. Although characterised based on equilibrated samples, this behaviour is similar to that from the derivative of thermal energy by slow cooling using standard MD simulations (see the inset of Fig...
generation of M configurations according to the Metropolis algorithm (in a NVT or a NPT ensemble) or estimation of a corresponding number of time steps in a MD simulation 2. performing a number K of attempts to insert a (N + 1)st test particle at a random place in the simulation box ...
specific protein regions, to large-scale domain rearrangements. Quantitatively, BioEmu samples protein conformations with relative free energy errors around 1 kcal/mol, as validated against millisecond-timescale MD simulation and experimentally-measured protein stabilities....
In the present work using molecular dynamics (MD) simulation method we investigate the dynamical and structural behavior of CaTiO3 perovskite at normal pressure and temperature conditions. The MD calculations were performed on a system of 16,000 particles (3200Ca + 3200Ti + 96,00O), initially ...