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 …

Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

The Tinker software, currently released as version 8, is a modular molecular mechanics and
dynamics package written primarily in a standard, easily portable dialect of Fortran 95 with …

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

A software framework is introduced that facilitates the application of biasing algorithms to
collective variables of the type commonly employed to drive massively parallel molecular …

This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files …

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

Since its inception nearly a half century ago, CHARMM has been playing a central role in
computational biochemistry and biophysics. Commensurate with the developments in …

Cyclosporins are natural or synthetic undecapeptides with a wide range of actual and
potential pharmaceutical applications. Several members of the cyclosporin compound family …

Conspectus The observation of complex structural transitions in biological and abiological
molecular objects within time scales amenable to molecular dynamics (MD) simulations is …