Related papers: Tunneling-splittings from path-integral molecular …
We introduce an approach for calculating perturbative corrections to the ring-polymer instanton approximation to tunneling splittings (RPI+PC), by computing higher-order terms in the asymptotic expansion in $\hbar$. The resulting method…
We examine the formulation and numerical treatment of dissipative particle dynamics (DPD) and momentum-conserving molecular dynamics. We show that it is possible to improve both the accuracy and the stability of DPD by employing a pairwise…
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed…
Protein-ligand (un)binding simulations are a recent focus of biased molecular dynamics simulations. Such binding and unbinding can occur via different pathways in and out of a binding site. We here present a theoretical framework how to…
Massively parallel computer architectures create new opportunities for the performance of long-timescale molecular dynamics (MD) simulations. Here, we introduce the path-accelerated molecular dynamics (PAMD) method that takes advantage of…
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…
Coarse-graining of fully atomistic molecular dynamics simulations is a long-standing goal in order to allow the description of processes occurring on biologically relevant timescales. For example, the prediction of pathways, rates and…
Because most chemical or biological experiments are performed under conditions of controlled pressure and temperature, it is important to simulate the isobaric-isothermal ensemble at the atomic level to reveal the microscopic mechanism. By…
This work combines state-of-the-art machine learning techniques with highest-level electronic structure calculations and full-dimensional quantum tunneling calculations to obtain a quantitative characterization of tunneling splittings for…
Accounting for nuclear quantum effects (NQEs) can significantly alter material properties at finite temperatures. Atomic modeling using the path-integral molecular dynamics (PIMD) method can fully account for such effects, but requires…
We present a new method of conducting molecular dynamics simulation in isothermal-isobaric ensemble based on Langevin equations of motion. The stochastic coupling to all particle and cell degrees of freedoms is introduced in a correct way,…
A methodology to sample the isothermal-isobaric ensemble using Langevin dynamics is proposed, which combines novel features of geometric integrators for the equations of motion. By employing the Trotter expansion, the methodology generates…
Building on Paper I of this series, which introduced path integral Monte Carlo (PIMC) estimators for the derivative of the potential of mean force (PMF), we propose two path integral molecular dynamics (PIMD) integrators that can make use…
In this work, a novel ring polymer representation for multi-level quantum system is proposed for thermal average calculations. The proposed presentation keeps the discreteness of the electronic states: besides position and momentum, each…
Machine learning (ML) methods provide advanced means for understanding inherent patterns within large and complex datasets. Here, we employ the principal component analysis (PCA) and the diffusion map (DM) techniques to evaluate the glass…
Dissipative Particle Dynamics (DPD) is a popular simulation model for investigating hydrodynamic behavior of systems with non-negligible equilibrium thermal fluctuations. DPD employs soft core repulsive interactions between the system…
An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD) [J. Chem.…
Path-integral molecular dynamics (PIMD) simulations are crucial for accurately capturing nuclear quantum effects in materials. However, their computational intensity and reliance on multiple software packages often limit their applicability…
Most recently, path integral molecular dynamics (PIMD) has been successfully applied to perform simulations of identical bosons and fermions by B. Hirshberg et al.. In this work, we demonstrate that PIMD can be developed to calculate…
Path integral quantum Monte Carlo (PIMC) is a method for estimating thermal equilibrium properties of stoquastic quantum spin systems by sampling from a classical Gibbs distribution using Markov chain Monte Carlo. The PIMC method has been…