相关论文: Quasi-Hamiltonian Equations of Motion for Internal…

For many biological applications of molecular dynamics (MD) the importance of good sampling in conformational space makes it necessary to eliminate the fastest motions from the system in order to increase the time step. An accurate…

We present the molecular hyperdynamics algorithm and its implementation to the nonorthogonal tight-binding model NTBM and the corresponding software. Due to its multiscale structure, the proposed approach provides the long time scale…

Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…

Molecular dynamics (MD) simulations are used in biochemistry, physics, and other fields to study the motions, thermodynamic properties, and the interactions between molecules. Computational limitations and the complexity of these problems,…

Molecular dynamics simulations are used to study structure formation in simple model polymer chains that are subject to excluded volume and torsional interactions. The changing conformations exhibited by chains of different lengths under…

Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions…

Molecular dynamics simulates the~movements of atoms. Due to its high cost, many methods have been developed to "push the~simulation forward". One of them, metadynamics, can hasten the~molecular dynamics with the~help of variables describing…

The internal dynamics of macro-molecular systems is characterized by widely separated time scales, ranging from fraction of ps to ns. In ordinary molecular dynamics simulations, the elementary time step dt used to integrate the equation of…

Internal coordinate molecular dynamics (ICMD) is an efficient method for studying biopolymers, but it is readily applicable only to molecules with tree topologies, that is with no internal flexible rings. Common examples violating this…

The integration time step is a critical determinant of performance in molecular dynamics simulations, governing the trade-off between speed and fidelity. Although 2 fs remains the standard in atomistic biomolecular simulations, the push for…

This work reports numerical experiments intended to clarify the internal equilibration process in large molecules, following vibrational excitation. A model of amorphous and oxygenated hydrocarbon macromolecule (about 500 atoms)--simulating…

Computational chemistry allows researchers to experiment in sillico: by running a computer simulations of a biological or chemical processes of interest. Molecular dynamics with molecular mechanics model of interactions simulates N-body…

The role of internal motions and molecular geometry on $^1$H NMR relaxation times $T_{1,2}$ in hydrocarbons is investigated using MD (molecular dynamics) simulations of the autocorrelation functions for in{\it tra}molecular $G_R(t)$ and…

Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly…

An approximate approach to quantum vibrational dynamics, "Brownian Chain Molecular Dynamics (BCMD)", is proposed to alleviate the chain resonance and curvature problems in the imaginary time-based path integral (PI) simulation. Here the…

A Monte Carlo method for dynamics simulation of all-atom protein models is introduced, to reach long times not accessible to conventional molecular dynamics. The considered degrees of freedom are the dihedrals at C$_\alpha$-atoms. Two Monte…

Bosonic exchange symmetry leads to fascinating quantum phenomena, from exciton condensation in quantum materials to the superfluidity of liquid Helium-4. Unfortunately, path integral molecular dynamics (PIMD) simulations of bosons are…

Molecular dynamics (MD) simulations provide atomistic insights into the structure, dynamics, and function of biomolecules by generating time-resolved, high-dimensional trajectories. Analyzing such data benefits from estimating the minimal…

Developing efficient path integral (PI) methods for atomistic simulations of vibrational spectra in heterogeneous condensed phases and interfaces has long been a challenging task. Here, we present the h-CMD method, short for hybrid centroid…

Including quantum mechanical effects on the dynamics of nuclei in the condensed phase is challenging, because the complexity of exact methods grows exponentially with the number of quantum degrees of freedom. Efforts to circumvent these…