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MetaD_EXE_TestSys

DOI

Update

This repository has been outdated and is no longer under maintenance. The work has been migrated to the new project repository alchemical_metadynamics. The work has been published in the Journal of Chemical Theory and Computation, titled Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free energy calculations.

Description

This is a repository for hosting the simulation files of the test systems for the development of MetaD-EXE sampling method. Important directories include:

  • Tutorials: a quick tutorial about using PLUMED to post-process a trajectory and to perform different variants of metadynamics, including standard metadynamics, well-tempered metadynamics, multi-dimensional metadynamics and multiple walkers metadynamics.
  • Research_Notes: Notes of simulation details of all tests in different test systems and minutes of meetings.
  • System1: A directory for Test system 1, which is an argon atom in a water box.
    • System1/Prep: A directory for the preparation of the simulation input files for each test.
    • System1/Test_1: Comparison of the results of expanded ensemble simulation of with weights fixed at 0 (EXE_fixed) with standard alchemical metadynamics with 0 biases.
    • System1/Test_2: Comparison of the results of expanded ensemble simulation with updating weights (wl-scale=0.999999) with standard alchemical metadynamics.
    • System1/Test_3: Comparison of the results of expanded ensemble simulation with updating weights (wl-scale=0.8) with well-tempered alchemical metadynamics.
  • System2: A directory for Test system 2, which is a lactic acid in a water box.
    • System2/Prep: A directory for the preparation of the simulation input files for each test.
    • System2/Test_1: Comparison the results of vanilla simulations at fixed lambda states with standard alchemical metadynamics with 0 biases.
    • System2/Test_2: Comparison the results of expanded ensemble simulation with updating weights (wl-scale=0.999999) with standard alchemical metadynamics.
    • System2/Test_3: Comparison of the results of expanded ensemble simulation with updating weights (wl-scale=0.8) with well-tempered alchemical metadynamics.
  • System3: A directory for Test system 3, which is CB8-G3 host-guest binding complex in the water box.
    • System3/Prep: A directory for the preparation of the simulation input files for each test (System3/Test_1).
    • System3/Test1: Comparison of the results of 1-dimensional metadynamics biasing the number of water molecules in the binding cavity with alchemical metadynamics/

For more details about the file preparations and the simulations, please refer to the research note hosted on HackMD.