Dataset for Dual-Site Recognition in Classic DNA Aptamer

This is a simulation dataset for molecular dynamics studying the dual-site recognition mechanism of a classical DNA aptamer. All data were generated using the simulation engine Gromacs 2021.4 with the Colvars module patched and accelerated with GPU (NVIDIA 3070). In the uploaded compressed file, the "mdp" folder contains the mdp files used during the simulation, as well as the topology files and force field parameters, mainly generated through the CHARMM-GUI program. "1AMP22" represents Site 1/AMP, "1AMP9" represents Site 2/AMP, and "2AMP" represents Sites 1, 2/2AMP models. The suffix "eq" indicates equilibrium simulations, "d" indicates 1-dimensional enhanced sampling simulations using distance as a collective variable, "dphi" indicates 2-dimensional enhanced sampling simulations using distance and flip angle as collective variables, and "co" indicates enhanced sampling simulations with both AMP ligands recognizing simultaneously.