Search results for "molecular dynamics"
showing 10 items of 1075 documents
An efficient β-turn directed cyclization of simple peptidomimetics
1999
Abstract Chiral polyaza[n]para- and metacyclophanes are easily assembled starting from the appropriate bis(bromomethyl)arene and diamides obtained from aminoacids and alkylidenediamines. The corresponding ortho-derivatives could not be obtained. Molecular dynamics calculations suggest that those results can be explained through the participation of a β-turn like structure in the open chain intermediate, which is only important for para- and meta-derivatives.
Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics.
2011
A methodology for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and validated for acetone-methanol and acetone-tetrachloromethane liquid mixtures. Fick diffusivities are obtained from Maxwell-Stefan (MS) diffusivities and the so-called thermodynamic factor. MS diffusivities describe the friction between different components, while the thermodynamic factor is the concentration derivative of the activity describing the deviation from ideal mixing behavior. It is important to note that all mutual diffusion experiments measure Fick diffusion coefficients, while molecular simulation provides MS diffusivities. The required thermodynamic fa…
United Atom Force Field for Molecular Dynamics Simulations of 1,4-Polybutadiene Based on Quantum Chemistry Calculations on Model Molecules
1998
We present a united atom force field for simulations of 1,4-polybutadiene based on ab initio quantum chemistry calculations on model molecules. The geometries and energies of conformers and rotational energy barriers in model alkenes and dienes have been determined from high-level quantum chemistry calculations. A rotational isomeric state (RIS) model for 1,4-polybutadiene based on the conformer geometries and energies of the model molecules has been derived. The characteristic ratio and its temperature dependence for cis-1,4-polybutadiene and trans-1,4-polybutadiene, and the characteristic ratio of a random copolymer of cis and trans units, as predicted by the RIS model, are in good agreem…
Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation
2014
We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results …
Multiple time step integrators and momentum conservation
1997
Abstract By use of the standard Liouville operator formalism, we derive a new symplectic multiple time step integrator for Hamiltonian systems with disparate masses, which, in contrast to previous algorithms, conserves the total momentum exactly, and is only moderately slower. The new scheme is tested numerically by application to Molecular Dynamics simulations of a polymer melt whose monomers have different masses, and compared to earlier algorithms.
Millimeter-Scale and Billion-Atom Reactive Force Field Simulation on Sunway Taihulight
2020
Large-scale molecular dynamics (MD) simulations on supercomputers play an increasingly important role in many research areas. With the capability of simulating charge equilibration (QEq), bonds and so on, Reactive force field (ReaxFF) enables the precise simulation of chemical reactions. Compared to the first principle molecular dynamics (FPMD), ReaxFF has far lower requirements on computational resources so that it can achieve higher efficiencies for large-scale simulations. In this article, we present our efforts on scaling ReaxFF on the Sunway TaihuLight Supercomputer (TaihuLight). We have carefully redesigned the force analysis and neighbor list building steps. By applying fine-grained …
Nucleation of quasicrystals by rapid cooling of a binary melt: A molecular-dynamics study.
1995
A binary Lennard-Jones fluid was cooled in an NPT ensemble by molecular-dynamics simulations. Depending on the cooling rate, we find a sharp transition from the melt either into a disordered structure or into a phase of icosahedral long-range order. We also observed a decagonal phase.
Performance of Different Force Fields in Force Probe Simulations
2013
We present detailed force probe molecular dynamic simulations of mechanically interlocked dimeric calix[4]arene-catenanes, comparing the results obtained using three different commonly used force fields (GROMOS G53a5, OPLS-AA, and AMBER GAFF). The model system is well characterized as a two-state system consisting of a closed compact and an elongated structure. Both states are stabilized by a different hydrogen-bond network, and complete separation of the dimer is prevented by the mechanical lock of the entangled aliphatic loops. The system shows fully reversible rebinding meaning that after bond rupture the system rejoins when the external force is relaxed. We present a detailed study of q…
Tetraaza-2,2′-biphenylophanes: larger is not always more flexible. The role of intramolecular H-bonding in polyazamacrocycles
2002
Abstract Intramolecular H-bonding can explain the trends in conformational flexibility for tetraaza-2,2′-biphenylophanes obtained by NMR and molecular dynamics calculations.
Local structure and dynamics of wurtzite‐type ZnO from simulation‐based EXAFS analysis
2014
Conventional methods of EXAFS data analysis are often limited to the nearest coordination shells of the absorbing atom due to the difficulties in accurate accounting for the so-called multiple-scattering effects. Besides, it is often difficult to resolve the non-equivalent groups of atoms in a single coordination shell due to strong correlation between structural parameters. In this study we overcome these problems by applying two different simulation-based methods, i.e., classical molecular dynamics (MD) and reverse Monte with evolutionary algorithm (EA), to the analysis of the Zn K-edge EXAFS data for wurtzite-type bulk ZnO. The RMC/EA-EXAFS method allowed us to separate the contributions…