Related papers: Infinite swapping replica exchange molecular dynam…
Because of growing interest in temperature-based sampling methods like replica exchange, this note aims to make some observations and raise some potentially important questions which we have not seen addressed sufficiently in the…
The ring-polymer molecular dynamics (RPMD) was used to calculate the thermal rate coefficients of the two-channel roaming reaction H + MgH. Both reaction channels, tight and roaming, are explicitly considered. This is a pioneering attempt…
Machine learning potentials have emerged as a means to enhance the accuracy of biomolecular simulations. However, their application is constrained by the significant computational cost arising from the vast number of parameters compared to…
In recent years, constant applied potential molecular dynamics has allowed to study the structure and dynamics of the electrochemical double-layer of a large variety of nanoscale capacitors. Nevertheless it remained impossible to simulate…
Swap algorithms can shift the glass transition to lower temperatures, a recent unexplained observation constraining the nature of this phenomenon. Here we show that swap dynamic is governed by an effective potential describing both particle…
We previously developed an algorithm, called resolution exchange, which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations[1]. Here, we demonstrate a generally…
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 propose a new method for estimating rare event probabilities when independent samples are available. It is assumed that the underlying probability measures satisfy a large deviations principle with a scaling parameter $\varepsilon$ that…
Ring polymer molecular dynamics (RPMD) is an accurate method for calculating thermal chemical reaction rates. It has recently been discovered that low-temperature calculations are strongly affected by the simulation parameters. Here, for…
We extend ring-polymer molecular dynamics (RPMD) to allow for the direct simulation of general, electronically non-adiabatic chemical processes. The kinetically constrained (KC) RPMD method uses the imaginary-time path-integral…
We introduce a new update scheme to systematically improve the efficiency of parallel tempering simulations. We show that by adapting the number of sweeps between replica exchanges to the canonical autocorrelation time, the average…
We use molecular dynamics simulations to study the dynamics of an ensemble of interacting self-propelled semi-flexible polymers in contact with a thermal bath. Our intention is to model complex systems of biological interest. We find that…
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…
We develop an algorithm suitable for parallel molecular dynamics simulations in $d$ spatial dimensions and describe its implementation in C++. All routines work in arbitrary $d$; the maximum simulated $d$ is limited only by available…
An investigation to optimize the application of the third-generation charge optimized many-body (COMB3) interatomic potential and associated input parameters was carried out through the study of solid-liquid interactions in classical…
This letter highlights the entropy exchange phenomenon in a coupled binary inter-correlating system following Haldane's non-linear statistical correlation. A unique coupling between a classical and a quantum-like system at the marginal…
We introduce mapping-variable ring polymer molecular dynamics (MV-RPMD), a model dynamics for the direct simulation of multi-electron processes. An extension of the RPMD idea, this method is based on an exact, imaginary time path-integral…
The ring polymer molecular dynamics (RPMD) rate theory is an efficient and accurate method for estimating rate coefficients of chemical reactions affected by nuclear quantum effects. The commonly used RPMD treatment of gas-phase bimolecular…
The computer simulation of many molecular processes is complicated by long time scales caused by rare transitions between long-lived states. Here, we propose a new approach to simulate such rare events, which combines transition path…
Ring polymer molecular dynamics (RPMD) has proven to be an accurate approach for calculating thermal rate coefficients of various chemical reactions. For wider application of this methodology, efficient ways to generate the underlying…