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](analyzer.mdfast-like-a-rocket) (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