This Review explores the dynamic behavior of water within nanopores and biological
channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside …

Water is a unique solvent that is ubiquitous in biology and present in a variety of solutions,
mixtures, and materials settings. It therefore forms the basis for all molecular dynamics …

Accurate modeling of the solvent environment for biological molecules is crucial for
computational biology and drug design. A popular approach to achieve long simulation time …

Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP)
remain a challenge: widely used,“general purpose” water models tend to favor overly …

The affinity of drug molecules to their respective molecular targets can be described by the
thermodynamic properties of the molecular interaction. These properties typically reflect the …

Despite the relevance of properly setting ionic concentrations in Molecular Dynamics (MD)
simulations, methods or practical rules to set ionic strength are scarce and rarely …

Implicit solvent models are essential for molecular dynamics simulations of biomolecules,
striking a balance between computational efficiency and biological realism. Efforts are …

Molecular dynamics simulations are an invaluable tool to characterize the dynamic motions
of proteins in atomistic detail. However, the accuracy of models derived from simulations …

Computer simulation provides an increasingly realistic picture of large-scale conformational
change of proteins, but investigations remain fundamentally constrained by the femtosecond …

Despite the development of massively parallel computing hardware including inexpensive
graphics processing units (GPUs), it has remained infeasible to simulate the folding of …