Related papers: ms2: A molecular simulation tool for thermodynamic…
Methods that combine collective variable (CV) based enhanced sampling and global tempering approaches are used in speeding-up the conformational sampling and free energy calculation of large and soft systems with a plethora of energy…
Artificial Intelligence predicts drug properties by encoding drug molecules, aiding in the rapid screening of candidates. Different molecular representations, such as SMILES and molecule graphs, contain complementary information for…
Molecular dynamics (MD) simulations allow investigating the structural dynamics of biomolecular systems with unrivaled time and space resolution. However, in order to compensate for the inaccuracies of the utilized empirical force fields,…
A recently proposed method for computer simulations in the isothermal-isobaric (NPT) ensemble, based on Langevin-type equations of motion for the particle coordinates and the ``piston'' degree of freedom, is re-derived by straightforward…
Theoretical concepts in condensed matter physics are typically verified and also developed by exploiting computer simulations mostly in simple models. Predictions based on these usually isotropic models are often at odds with measurement…
We present version 2.3 of SModelS, a public tool for the fast reinterpretation of LHC searches for new physics on the basis of simplified-model results. The main new features are a database update with the latest available experimental…
The symbolic manipulation program FORM is specialized to handle very large algebraic expressions. Some specific features of its internal structure make FORM very well suited for parallelization. We have now two parallel versions of FORM,…
This chapter discusses how the PLUMED plugin for molecular dynamics can be used to analyze and bias molecular dynamics trajectories. The chapter begins by introducing the notion of a collective variable and by then explaining how the free…
Accelerated molecular dynamics (MD) simulations are implemented to model the sliding process of AFM experiments at speeds close to those found in experiment. In this study the hyperdynamics method, originally devised to extend MD time…
The authors propose a robust semi-parametric empirical likelihood method to integrate all available information from multiple samples with a common center of measurements. Two different sets of estimating equations are used to improve the…
In this work, based on the cluster expansion of the energy functional, we have extracted a formalism for calculation of the thermodynamic properties of fluids with non-spherical molecules. The salient feature of the extracted formalism is…
Universal machine-learning interatomic potentials (uMLIPs) enable reactive molecular simulations with near-DFT accuracy, yet applying them efficiently to large, realistic condensed-phase systems remains computationally demanding. Here we…
We investigate the structural and dynamical properties of binary aluminum-titanium liquid metallic alloys, as a function of temperature and composition. We make use of MD-simulations, using a transferable machine-learning potential…
Molecular dynamics (MD) simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules but are limited by the timescale barrier, i.e., we may be unable to efficiently obtain properties because we need to run…
Sampling from the full posterior distribution of high-dimensional non-linear, non-Gaussian latent dynamical models presents significant computational challenges. While Particle Gibbs (also known as conditional sequential Monte Carlo) is…
We present here two novel algorithms for simulated tempering simulations, which break detailed balance condition (DBC) but satisfy the skewed detailed balance to ensure invariance of the target distribution. The irreversible methods we…
The miscibility in several polymer blend mixtures (polymethylmethacrylate/polystyrene, (1,4-cis) polyisoprene/polystyrene, and polymethylmethacrylate/polyoxyethylene) has been investigated using Molecular Dynamics simulations for atomistic…
Machine-learned interatomic potentials (MLIPs) show promise in accurately describing the physical properties of materials, but there is a need for a higher throughput method of validation. Here, we demonstrate using that MLIPs and molecular…
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…
Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…