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gmx_MMPBSA v1.5.5 (06/10/2022)

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@marioernestovaldes marioernestovaldes released this 10 Jun 22:20
· 379 commits to master since this release
v1.5.5
bf07152

gmx_MMPBSA v1.5.5 (06/10/2022)

Additions

gmx_MMPBSA

  • Improved the API (#209)
    • Added a new method to get the Enthalpy
    • Added a new method to get the Entropy
    • Added a new method to get the Binding
    • Added a new method to get the Decomposition energy
    • Added a new method to get the gmx_MMPBSA_ana data

gmx_MMPBSA_ana

  • Added multiprocessing and multithreading (#209)
  • Wait indicator
  • Added Error line cap size
  • Systems, subsystems and component selection options
  • Added threshold to remove energetic terms or residues
  • Correlation (#137)
    • Normal correlation using ΔG
    • Mutant correlation using ΔΔG
    • Energy values table
    • Interactive systems selection and Experimental Ki editor
    • New regression plot with bivariate and univariate graphs
    • Chart options panel
      • General options
      • Regression options
        • Scatter
        • Distribution

Documentation

  • News section
  • Animated command-line code block with terminal
  • Added versioning
  • Added installation using *.yml configuration file (#221)
  • Added a new tutorial for correlation analysis (#194)

Fix

gmx_MMPBSA_ana

  • Close gmx_MMPBSA_ana properly when the selection dialog is rejected

  • Compatibility with previous versions (< v1.5.2)

  • Added several tooltips

  • Improved general performance. See the benchmark (#209, #230, #243)

    • Improved the reading of output files and optimized data storage. (#228)
    • Eliminated the recalculation of IE and C2 entropies before opening the GUI. Now read from outputs files
    • Optimized data storage and access to subsets in panda's Dataframes
    • Now file processing and graphics generation does not freeze the GUI.
    • Removed redundant steps and data
    • Removed line graphs for components in the per-wise decomposition schema
    • Data access, processing, and storage are done in the API.
    • Added the option to temporarily store data on the hard disk instead of memory
    • Removed several pop-up windows
    • Decreased RAM consumption

  • Removed H5 support

  • Invalid periodicity in the prmtop (#211)

  • Buffer saturation (#213)

Changes

gmx_MMPBSA

  • Improved IE and C2 calculation

gmx_MMPBSA_ana

  • Change the IE representation

  • Removed summary widget

  • Now the bar plot data contain the Average, SD, and SEM instead of all frames

  • Chart Options

    • Error line color
    • Error line representation (SD or SEM)

  • Restructured the init (system selection) dialog

    • Improved energy and decomposition options selection
    • Improved the correlation options
    • Added a new section for performance configuration
    • Added RAM consumption estimator
    • Improved the systems' tree representation and edition options

gmx_MMPBSA_test

  • The examples folder moved up to the root directory
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