Related papers: Hamiltonian replica-exchange in GROMACS: a flexibl…
Improving time-to-solution in molecular dynamics simulations often requires strong scaling due to fixed-sized problems. GROMACS is highly latency-sensitive, with peak iteration rates in the sub-millisecond, making scalability on…
We develop a computational method to learn a molecular Hamiltonian matrix from matrix-valued time series of the electron density. As we demonstrate for three small molecules, the resulting Hamiltonians can be used for electron density…
The widespread popularity of replica exchange and expanded ensemble algorithms for simulating complex molecular systems in chemistry and biophysics has generated much interest in enhancing phase space mixing of these protocols, thus…
We describe a simple, efficient method for simulating Hamiltonian dynamics on a quantum computer by approximating the truncated Taylor series of the evolution operator. Our method can simulate the time evolution of a wide variety of…
In a previous paper [3] we have studied flows defined on polytopes, presenting a new method to encapsulate its asymptotic dynamics along the edge-vertex heteroclinic network. These results apply to the class of polymatrix replicator…
The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these…
Efficient computational methods that are capable of supporting experimental measures obtained at constant values of pH and redox potential are important tools as they serve to, among other things, provide additional atomic level information…
We combined the genetic crossover, which is one of the operations of genetic algorithm, and replica-exchange method in parallel molecular dynamics simulations. The genetic crossover and replica-exchange method can search the global…
We present an implementation of alchemical free energy simulations at the quantum mechanical level by directly interpolating the electronic Hamiltonian. The method is compatible with any level of electronic structure theory and requires…
We investigate to what extend the replica-exchange Monte Carlo method is able to equilibrate a simple liquid in its supercooled state. We find that this method does indeed allow to generate accurately the canonical distribution function…
The Hamiltonian Monte Carlo (HMC) method allows sampling from continuous densities. Favorable scaling with dimension has led to wide adoption of HMC by the statistics community. Modern auto-differentiating software should allow more…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
A novel error measure, referred to as the hysteresis error, is developed from the Crooks fluctuation theorem to evaluate sampling quality in free energy calculations. Theory and numerical free energy of hydration calculations are used to…
Development of computer technology in chemistry, bring many application of chemistry. Not only the application to visualize the structure of molecule but also to molecular dynamics simulation. One of them is Gromacs. Gromacs is an example…
We investigate a generic, parallel replica-exchange framework for Monte Carlo simulations based on the Wang-Landau method. To demonstrate its advantages and general applicability for massively parallel simulations of complex systems, we…
Relative free energy calculations are now widely used in academia and industry, but the accuracy is often limited by poor sampling of the complexes conformational ensemble. To address this, we have developed a novel method termed…
Hybrid particle-field molecular dynamics combines standard molecular potentials with density-field models into a computationally efficient methodology that is well-adapted for the study of mesoscale soft matter systems. Here, we introduce a…
We propose an algorithm for simulating the dynamics of a geometrically local Hamiltonian $A$ under a small geometrically local perturbation $\alpha B$. In certain regimes, the algorithm achieves the optimal scaling and outperforms the…
Application of the adiabatic model of quantum computation requires efficient encoding of the solution to computational problems into the lowest eigenstate of a Hamiltonian that supports universal adiabatic quantum computation. Experimental…
Efficient sampling from high-dimensional distributions is a challenging issue which is encountered in many large data recovery problems involving Markov chain Monte Carlo schemes. In this context, sampling using Hamiltonian dynamics is one…