Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of "lagged RMSD-analysis" as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δ...

The advances in theory and computing technology over the last decade have led to enormous progress in applying atomistic molecular dynamics (MD) methods to the characterization, prediction, and design of chemical, biological, and material systems. MD simulation of very large systems are currently being performed by using massively parallel architectures. However, there is a fundamental difficul...

Molecular dynamics (MD) simulation has been carried out to study dynamical stability of intra-protein hydrogen bonds based on two set of atomic charges, the standard AMBER charge and the polarized protein-specific charge (PPC). The latter is derived from quantum mechanical calculation for protein in solution using a recently developed molecular fractionation with conjugate caps-Poisson-Boltzman...

We present a simple method for calculating a continuum temperature field directly from a molecular dynamics (MD) simulation. Using the idea of a projection matrix previously developed for use in the bridging scale, we derive a continuum temperature equation which only requires information that is readily available from MD simulations, namely the MD velocity, atomic masses and Boltzmann constant...

The numerical simulation of a Poiseuille flow in a narrow channel using the molecular dynamics simulation (MDS) is performed. Poiseuille flow of liquid Argon in a nanochannel is simulated by embedding the fluid particles in a uniform force field. Density, velocity and Temperature profiles across the channel are investigated. When particles will be inserted into the flow, it is expected that the...

A parallel programming library for molecular dynamics (MD) simulations is described and applied to the recently proposed split integration symplectic method (SISM) for MD simulation. The results show that for a system of 1024 linear chain molecules with an integration step of 4.5 fs parallel execution of SISM with the particle–particle interactions (PPIs) library on 32 computers gives efficienc...

We present mesoscopic simulations of the counterion-induced electro-osmotic flow in different electrostatic coupling regimes. Two simulation methods are compared, dissipative particle dynamics (DPD) and coupled lattice-Boltzmann/molecular dynamics (LB/MD). A general mapping scheme to match DPD to LB/MD is developed. For the weak coupling regime, analytic expressions for the flow profiles in the...

A hybrid molecular-dynamics (MD) and finite-element simulation approach is used to study stress distributions in silicon/silicon-nitride nanopixels. The hybrid approach provides atomistic description near the interface and continuum description deep into the substrate, increasing the accessible length scales and greatly reducing the computational cost. The results of the hybrid simulation are i...

Structure and dynamics are essential elements of protein function. Protein structure is constantly fluctuating and undergoing conformational changes, which are captured by molecular dynamics (MD) simulations. We introduce a computational framework that provides a compact representation of the dynamic conformational space of biomolecular simulations. This method presents a systematic approach de...

I derive a general method for accelerating the molecular-dynamics (MD) simulation of infrequent events in solids. A bias potential (DVb) raises the energy in regions other than the transition states between potential basins. Transitions occur at an accelerated rate and the elapsed time becomes a statistical property of the system. DVb can be constructed without knowing the location of the trans...