Skip to content

Comparison of gmx_MMPBSA with other programs

This comparison is based on each program's documentation.

Calculation features

Feature g_mmpbsa GMXPBSA 2.1 MMPBSA.py 1 gmx_MMPBSA
Normal binding free energies PB PB PB 11 and GB PB 11 and GB
* GB models 1, 2, 5, 7 and 8 1, 2, 5, 7, 8 and NSR6
Stability
Alanine scanning 2
Entropy corrections 3 NMODE and QH NMODE, IE, and C2; legacy QH reader
Decomposition schemes Per-Residues Per-Residues and Per-Wise Per-Residues and Per-Wise
QM/MMGBSA
MM/3D-RISM
Membrane-protein support
Approximations ST ST and MT ST and MT ST and MT

Analysis features

Feature g_mmpbsa GMXPBSA 2.1 MMPBSA.py 1 gmx_MMPBSA
API
Analyzer Tool 4
* Multiple systems at once
* Correlation between systems
* Per-residue energies to PDB
* Interactive visualization
** 3D Molecular Visualization PyMOL
** Interactive Charts static image
* Plotting tool internal tools API and graphics library 5 gmx_MMPBSA_ana
* Energetic Terms charts ΔGpolar, ΔGnonpolar, ΔEMM and ΔGbind All
* Export data to CSV file
** Energy Summary
** Individual Energetic Terms

Technical features

Feature g_mmpbsa GMXPBSA 2.1 MMPBSA.py 1 gmx_MMPBSA
GROMACS Version 4.x, 5.x and 2016+ 6 4.x, 5.x and 20xx.x 7 --- Any compatible version 10
Dependencies APBS (1.2.x, 1.3.x or 1.4.x) APBS (1.x.x) 8 AmberTools AmberTools 9
Parallel computation Depends on APBS Locally using APBS or in HPC divided in jobs
Steps for:
* Calculation and Summary Multiple Multiple One One
* Analysis Multiple Multiple Multiple One

  1. MMPBSA.py is included in the AMBER package ↩↩↩

  2. Without documentation ↩

  3. NMODE = normal-mode approximation, QH = quasi-harmonic approximation, IE = interaction entropy approximation, and C2 = C2 Entropy. In 1.7.0, new QH calculations are disabled; historical QH result files remain readable only during the compatibility window. ↩

  4. We plan to extend gmx_MMPBSA compatibility to MMPBSA.py's results ↩

  5. The AmberUtils repository provides tools for analyzing the results ↩

  6. GROMACS 20xx.x is not officially supported. A pull request provides limited compatibility with versions later than 2016.x ↩

  7. Support for GROMACS 20xx.x is not documented; the table assumes compatibility because the tool is script-based ↩

  8. Support for APBS 3.x.x is not documented ↩

  9. AmberTools executables are resolved from the active environment/PATH. The 1.7.0 tested and recommended conda range is >=24.8,<27, but other compatible AmberTools versions may also work when their Python and compiled dependency stack is consistent. ↩

  10. The 1.7.0 tested and recommended conda range is GROMACS >=2022,<2027, not a hard runtime limit. GROMACS executables can be supplied through PATH or gmx_path; conversion paths and force-field/model restrictions still apply. See compatibility and upgrades. ↩

  11. gmx_MMPBSA supports linear and nonlinear PB equations. MMPBSA.py, by contrast, requires the user to modify the *.mdin input files manually ↩↩

Last update: September 12, 2026 17:16:09
Created: February 8, 2021 07:10:13
Back to top