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@wehs7661 wehs7661 released this 02 Aug 22:23
· 365 commits to master since this release
0.7.0
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Learn about vigilant mode.

Several major changes have been made since the last release of version 0.6.0. Below we list all changes that would influence the way ensemble_md is used, in the order of decreasing importance.

  • Deployed the package to PyPI: https://pypi.org/project/ensemble-md/0.7.0/
  • ensemble_md has been enabled to work with MPI-enabled GROMACS.
  • Enabled coordinate modification/relative free energy calculations in the EEXE framework
    • See the project page to find the corresponding issues and PRs relevant to the work.
    • Added the YAML parameter modify_coords for specifying the external module for coordinate manipulation.
    • Added a predefined contract for the external module modify_coords
    • Enabled specifying different GRO and TOP input files.
    • Enabled specifying different MDP parameters for different replicas by adding the YAML parameter mdp_args.
    • Added the YAML parameter add_swappables to enable relative free energy calculations using EEXE.
  • Better parameter handling
    • Added restrictions for specifying nstlog and nstdhdl in the input MDP template
    • Added get_ref_dist to the class EnsembleEXE and modified update_MDP to fix the reference distance(s) for all iterations when distance restraint(s) are used. This solved the issue of poor sampling for the CB7-10 test system.
  • Enabled inverse variance weighting in weight combination
  • Added new functionalities to analyze_traj.py, including plot_g_vecs, get_swaps, plot_swaps, and stitch_trajs_for_sim
  • Modified functionalities
    • Converted identify_swappable_pairs into a static method
    • Modified explore_EEXE to allow estimating the chance of not having any swappable pairs
  • Removed map_lambda2state and the attributes lambda_dict and lambda_ranges
  • Fixed the bug so that executions on all ranks are terminated whenever is a GROMACS error in any child process
  • Several minor bug fixes in several functions, including get_averaged_weights, reformat_MDP, parse_log, and autoconvert
  • Updated the documentation

In the next release, we will focus more on refining functionalities for data analysis.

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