Improving Aptamer Binding Affinity for HN Protein of Newcastle Disease Virus: Molecular Dynamics Simulations and MM/GBSA Calculations studies

Data Description: (1) All data uploaded to this database only represent the input and output files of the current research, including files from two parts: molecular dynamics simulations and binding free energy calculations. (2) Due to the large size of the original dynamics trajectories and intermediate files generated during binding free energy calculations, which exceed 50GB and cannot be uploaded, we have cleaned the data. The dynamics trajectories have undergone periodic correction and elimination of translation and rotation (fit.xtc). (3) Additionally, we have provided parameter files, log files, tpr files, top files, etc., throughout the molecular dynamics simulation process. Researchers can reproduce the simulations at any time using the current parameter files. (4) The parameter files for the binding free energy calculation part have also been provided (mmpbsa.in). Other parameter files used can be found in the molecular dynamics simulation folder.