aMD (Accelerated molecular dynamics) is an enhanced-sampling method that improves the conformational space sampling by reducing energy barriers separating different states of a system. The method modifies the potential energy landscape by raising energy wells that are below a certain threshold level, while leaving those above this level unaffected. As a result, barriers separating adjacent energy basins are reduced, allowing the system to sample conformational space that cannot be easily accessed in a classical MD simulation. We provide NAMD implementation of aMD. Visit the NAMD website for complete information and documentation.
Please acknowledge the use of NBCR software: "This project was supported by grants from the National Center for Research Resources (5P41RR008605-19) and the National Institute of General Medical Sciences (P41 GM103426) from the National Institutes of Health"
aMD Citation: [plain text]