Many biologically important processes such as enzyme catalysis, signal transduction, ligand
binding and allosteric regulation occur on the micro-to millisecond time-scale. Despite the …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

Peptides mediate up to 40% of known protein–protein interactions in higher eukaryotes and
play an important role in cellular signaling. However, it is challenging to simulate both …

Background Accelerated molecular dynamics (aMD) has been proven to be a powerful
biasing method for enhanced sampling of biomolecular conformations on general-purpose …

Slow diffusive conformational transitions play key functional roles in biomolecular systems.
Our ability to sample these motions with molecular dynamics simulation in explicit solvent is …

A simple method is introduced to achieve efficient random walking in the energy space in
molecular dynamics simulations which thus enhances the sampling over a large energy …

Protein–protein interactions (PPIs) play key roles in many fundamental biological processes
such as cellular signaling and immune responses. However, it has proven challenging to …

Various advanced simulation techniques, which are used to sample the statistical ensemble
of systems with complex Hamiltonians, such as those displayed in condensed matters and …

We develop here the methodology for dramatically accelerating the ReaxFF reactive force
field based reactive molecular dynamics (RMD) simulations through use of the bond boost …

Improving the accuracy of molecular mechanics force field parameters for atomistic
simulations of proteins and nucleic acids has been an ongoing effort. The availability of …