Source code for "Optimal Enhanced Sampling of Protein Conformational Changes by Extract Reaction Coordinates from Energy Relaxation"

This set of files contain the custom code for the core results in the paper titled: Optimal Enhanced Sampling of Protein Conformational Changes by Extract Reaction Coordinates from Energy Relaxation. The results in this paper are mostly generated by a sequence of calculations using standard MD simulation packages (e.g. GROMACS): 1) MD simulation of energy relaxation of HIV protease and PDZ follow the standard procedures (Li et al, JCTC, 18, 5692 (2022); Sagnella et al, JPCB, 105, 7057 (2001)); 2) Calculation of the generalized work functional, which mainly involves outputting forces and velocities from GROMACS.

The custom algorithm is mainly the code to generate the RC-uncovered trajectories. The source codes and instructions to install and run are provided in the ‘readme_source.pdf’. In addition, a compiled executable and two example datasets are included as demo. Instructions to run the demo is in the ‘readme_demo.pdf’.