In silico tools, such as molecular docking, are widely applied to study interactions and
binding affinity of biological activity of proteins and peptides. However, restricted sampling of …

Enhanced sampling algorithms have emerged as powerful methods to extend the utility of
molecular dynamics simulations and allow the sampling of larger portions of the …

NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

We propose and discuss an efficient scheme for the in silico sampling for parts of the
molecular chemical space by semiempirical tight-binding methods combined with a meta …

Developing algorithmic approaches for the rational design and discovery of materials can
enable us to systematically find novel materials, which can have huge technological and …

The impact of molecular dynamics (MD) simulations in molecular biology and drug discovery
has expanded dramatically in recent years. These simulations capture the behavior of …

Computational techniques have been applied in the drug discovery pipeline since the
1980s. Given the low computational resources of the time, the first molecular modeling …

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

Although molecular dynamics simulations have become a useful tool in essentially all fields
of chemistry, condensed matter physics, materials science, and biology, there is still a large …

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