gmx_MMPBSA v1.6.4 (04/11/2024)

What's Changed

• Fixe Installations and dependences
• Fixing get_corrstd for small system changes by @LAndersen1 in #486
• Updating the versioneering library by @LAndersen1 in #488
• Corrected _temp_top.top behaviour to accommodate asynchronous scenarios by @ale94mleon in #493

New Contributors

• @LAndersen1 made their first contribution in #486
• @ale94mleon made their first contribution in #493

Full Changelog: v.1.6.3...1.6.4

gmx_MMPBSA v1.6.3 (02/19/2024)

Fixed minor issues in gmx_MMPBSA and gmx_MMPBSA_ana
Implemented the custom mask atom selection for qm-charge
Fixed inconsistencies with the installation process and the dependencies

gmx_MMPBSA v1.6.2 (09/14/2023)

Fixed minor issues

gmx_MMPBSA v1.6.1 (04/04/2023)

Fixes

• PB decomp ends in error (#352)
• Better parsing for errors

gmx_MMPBSA v1.6.0 (02/20/2023)

Additions

• GBNSR6 model implementation
  • Enthalpy
  • Per-residue and Per-wise decomposition
  • Documentation and examples
• Added git dependency to env.yml file
• Groups can now be defined as either the number or the name (#157)
• Added error tracking for groups that are not in the index file

Fixes

• Incompatible compilers version
• Fixed bug when CAS and PB/RISM calculations are performed
• Fixed duplicated options and args checking
• Documentation improved
• Fixed numpy deprecated np.float (#316)
• Fixed reproducible command line in debugging in log file (#335)
• GROMACS 2023 compatibility (#327, #335)
• Fixed IE and C2 Entropy (#325)
• PyMOL doesn't open within gmx_MMPBSA environment (#331)
• Inaccessible _temp_top.top when the topology file is in different directory (#299)

Changes

• A copy old info file is created when rewrite-output (for backward compatibility)
• Setting inp = 1 by default (#329)

gmx_MMPBSA v1.5.7 (09/10/2022)

Additions

• Progress bar implementation
• verbose options for API and info logging for IE and C2 entropy calculations
• Added logging info for MPI calculations

Fixes

• QH entropy calculation
• Decomposition bug (#269)
• Alanine scanning in Terminal residues
• Regression to output files subwindow in gmx_MMPBSA_ana
• Bug when using the compact results version
• Seaborn compatibility
• print_res in &decomp namelist does not accept "all" (#292)
• error when output files are open and any plot property is changed
• error if at least one residue of both the receptor and the ligand is not included in the selection for decomposition

Changes

• now use mpi4py when mpi_size > 1 otherwise use fake_MPI. Now "MPI" flag is not required

gmx_MMPBSA v1.5.6 (07/06/2022)

Fix

gmx_MMPBSA

• Inconsistent decomposition output (#246, #248)
• IE and C2 entropies calculation fail when rewrite-output (#253)
• Delta Delta Entropies' values are incorrect (#257)
• Loading binary file fails when alanine scanning is performed (#258)

gmx_MMPBSA_ana

• Mutant-Normal data is not computed or displayed (#254)
• Inconsistent energy values in PyMol visualization (#255)

Changes

gmx_MMPBSA

• Re-implementation of compact binary output file (#249)

gmx_MMPBSA v1.5.5 (06/10/2022)

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

gmx_MMPBSA v1.5.2 (03/23/2022)

Additions

gmx_MMPBSA

• ALPB (Analytical Linearized Poisson-Boltzmann) approximation (#170)
• PC+ correction in 3D-RISM (#187)
• Warning when using -deo option without &decomp namelist in the input file (#191)

gmx_MMPBSA_ana

• Tooltips for different options (#151)

Fix

gmx_MMPBSA_ana

• Chart options (#185)

Changes

gmx_MMPBSA

• 3D-RISM calculated with sander instead of rism3d.snglpnt (#153)

Documentation

• Update 3D-RISM doc (#190)

gmx_MMPBSA v1.5.1 (03/10/2022)

Additions

gmx_MMPBSA

• Add new variables for QM/MM calculations (#171)
• Improvement of "print_res" function for &decomp and QM (#150)
• Support for OPLS force field (#160)
• New precalculated .xvv files for 3D-RISM

gmx_MMPBSA_ana

• Support for PyQt6

Documentation

• gmx_MMPBSA_ana documentation (v1.5.0) (#152)
• Tutorial for psf_dcd files
• Tutorial for OPLS ff files

Fixes
gmx_MMPBSA

• Add ERROR when ligand.mol2 defined and no gaff or gaff2 in forcefields variable (#175)
• fixed incorrect path search when the gmx_path is defined
• Fixed error when no ions are included in the groups defined

gmx_MMPBSA_ana

• Remove empty terms issue (#179)
• fixed chart title for decomposition