The traditional computational modeling of protein structure, dynamics, and interactions
remains difficult for many protein systems. It is mostly due to the size of protein …

Coronavirus disease 2019 (COVID-19), due to infection by the severe acute respiratory
syndrome coronavirus 2 (SARS-CoV-2), is now causing a global pandemic. Aerosol …

Since the classical molecular dynamics simulator LAMMPS was released as an open source
code in 2004, it has become a widely-used tool for particle-based modeling of materials at …

Atomistic or ab initio molecular dynamics simulations are widely used to predict
thermodynamics and kinetics and relate them to molecular structure. A common approach to …

Dissipative particle dynamics (DPD) belongs to a class of models and computational
algorithms developed to address mesoscale problems in complex fluids and soft matter in …

The Martini model, a coarse-grained force field for biomolecular simulations, has found a
broad range of applications since its release a decade ago. Based on a building block …

The Martini coarse-grained force field has been successfully used for simulating a wide
range of (bio) molecular systems. Recent progress in our ability to test the model against …

The recent re‐parametrization of the Martini coarse‐grained force field, Martini 3, improved
the accuracy of the model in predicting molecular packing and interactions in molecular …

Computational modeling of biological systems is challenging because of the multitude of
spatial and temporal scales involved. Replacing atomistic detail with lower resolution …

By focusing on essential features, while averaging over less important details, coarse-
grained (CG) models provide significant computational and conceptual advantages with …