Accelerated Molecular Dynamics: Theory, Implementation and Applications

Accelerated molecular dynamics (aMD) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. Since it was first proposed by Hamelberg et al. (J. Chem. Phys., 120: 11919, 2004), the method has been applied to study a variety of biological and chemical problems. AMD is now available in several major molecular dynamics programs and its applications range from protein and lipid conformational sampling to ab initio and free energy calculations. Here we briefly review the development of the aMD method, focusing on its theory, implementation and applications. Through discussions of several examples, we also comment on potential directions of future development of the aMD method.