The Adaptively Biased Molecular Dynamics method revisited: New capabilities and an application

The free energy is perhaps one of the most important quantity required for describing biomolecular systems at equilibrium. Unfortunately, accurate and reliable free energies are notoriously difficult to calculate. To address this issue, we previously developed the Adaptively Biased Molecular Dynamics (ABMD) method for accurate calculation of rugged free energy surfaces (FES). Here, we briefly review the workings of the ABMD method with an emphasis on recent software additions, along with a short summary of a selected ABMD application based on the B-to-Z DNA transition. The ABMD method, along with current extensions, is currently implemented in the AMBER (ver.10-14) software package.