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

software
posted on 2023-07-28, 15:39 authored by Kenneth TsuiKenneth Tsui, Ao MaAo Ma, Huiyu Li

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’.

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