Atomistic simulation of the electrochemical double layer is an ambitious undertaking,
requiring quantum mechanical description of electrons, phase space sampling of liquid …

Gaussian accelerated molecular dynamics (GaMD) is a robust computational method for
simultaneous unconstrained enhanced sampling and free energy calculations of …

OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It
allows users to easily add new features, including forces with novel functional forms, new …

A Gaussian accelerated molecular dynamics (GaMD) approach for simultaneous enhanced
sampling and free energy calculation of biomolecules is presented. By constructing a boost …

Machine learning plays an important and growing role in molecular simulation. The newest
version of the OpenMM molecular dynamics toolkit introduces new features to support the …

Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of
conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they …

Nowadays, hybrid QM/MM approaches are widely used to study (supra) molecular systems
embedded in complex biological matrices. However, in their common formulation, mutual …

Bio-catalytic micro-and nanomotors self-propel by the enzymatic conversion of substrates
into products. Despite the advances in the field, the fundamental aspects underlying enzyme …

In this work, we critically assess the ability of the all-atom enhanced sampling method
accelerated molecular dynamics (aMD) to investigate conformational changes in proteins …

We characterized the landscape and drug sensitivity of ERBB2 (HER2) mutations in
cancers. In 11 datasets (n= 211,726), ERBB2 mutational hotspots varied across 25 tumor …