Supplementary Information for: Fundamental frequency from classical molecular dynamics

Influences of Small-Scale Effect and Boundary Conditions on the Free Vibration of Nano-Plates: A Molecular Dynamics Simulation

This paper addresses the influence of boundary conditions and small-scale effect on the free vibration of nano-plates using molecular dynamics (MD) and nonlocal elasticity theory. Based on the MD simulations, Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is used to obtain fundamental frequencies of single layered graphene sheets (SLGSs) which modeled in this paper as the mo...

Fundamental absorption frequencies and mean structures at vibrational ground state from quasi - classical direct ab initio MD : Triatomic molecule

Received 9 September 2007; in final form 20 December 2007 Abstract The fundamental frequencies and the mean values of the internal coordinates are extracted from the trajectories of classical dynamics based on the relation between the classical and the quantum mechanical frequencies using quasi-classical direct ab initio molecular dynamics, where the oscillator amplitude is specified by setting...

Epock: rapid analysis of protein pocket dynamics

SUMMARY The volume of an internal protein pocket is fundamental to ligand accessibility. Few programs that compute such volumes manage dynamic data from molecular dynamics (MD) simulations. Limited performance often prohibits analysis of large datasets. We present Epock, an efficient command-line tool that calculates pocket volumes from MD trajectories. A plugin for the VMD program provides a g...

Cryptic post-transition state bifurcations that reduce the efficiency of lactone-forming Rh-carbenoid C–H insertions† †Electronic supplementary information (ESI) available: Detailed molecular dynamics information, Cartesian coordinates, intrinsic reaction coordinates (IRCs), and 3-dimensional CYLview images of all optimized structures (PDF). See DOI: 10.1039/c6sc03745c Click here for additional data file.

Characterizing the structural ensemble of γ-secretase using a multiscale molecular dynamics approach† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc00980a Click here for additional data file.