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Stability calculations

This example evaluates the energy of a single protein-protein complex in stability mode. It uses the same solvated simulation, frame range, and GB-Neck2 model as the alanine-scanning and decomposition examples.

  • Calculation

    Single-system stability

  • System

    Protein-protein complex

  • Solvent model

    GB-Neck2 (igb=8)

  • Bundled test

    gmx_MMPBSA_test -t 13

Before you begin

The manual workflow uses the following files and selections:

  • Calculation settings

    mmpbsa.in (-i)

  • GROMACS system

    Structure com.tpr (-cs) and topology topol.top (-cp). Keep the toppar directory containing the referenced *.itp files beside topol.top.

  • Trajectory

    PBC-corrected and fitted trajectory com_traj.xtc (-ct)

  • Molecular selections

    Index index.ndx (-ci) with the SOLU_chain1 and SOLU_chain2 groups (-cg)

The two selected groups are combined to define the solute evaluated in stability mode. Receptor and ligand energy streams are not calculated. See the complete command-line reference for all options.

Run the example

Run the bundled test

The quickest way to reproduce this example is through the test runner:

gmx_MMPBSA_test -t 13

See the gmx_MMPBSA_test documentation for download, selection, and cleanup options.

Run it manually

Download the Stability example as a ZIP archive.

Extract the archive, change to the Stability directory, and choose either the serial or MPI command. You can also view the example files on GitHub before downloading them.

gmx_MMPBSA -O -s \
  -i mmpbsa.in \
  -cs com.tpr \
  -ct com_traj.xtc \
  -ci index.ndx \
  -cg SOLU_chain1 SOLU_chain2 \
  -cp topol.top \
  -o FINAL_RESULTS_MMPBSA.dat \
  -eo FINAL_RESULTS_MMPBSA.csv

mpirun -np 2 gmx_MMPBSA -O -s \
  -i mmpbsa.in \
  -cs com.tpr \
  -ct com_traj.xtc \
  -ci index.ndx \
  -cg SOLU_chain1 SOLU_chain2 \
  -cp topol.top \
  -o FINAL_RESULTS_MMPBSA.dat \
  -eo FINAL_RESULTS_MMPBSA.csv

Configure the calculation

The example uses the minimal mmpbsa.in shown first below. The all-options version was generated with gmx_MMPBSA --create_input gb and then adapted with the same example-specific values. The concise block is the runnable starting point; the generated block includes additional options and defaults, so the two blocks are not textually identical. Both blocks therefore describe the same calculation.

mmpbsa.in
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Sample input file for GB calculation
# This input provides a practical starting point for stability calculations.
# Review the model settings for your system and intended analysis.

&general
sys_name="Stability",
startframe=1,
endframe=10,
PBRadii=4,
/
&gb
igb=8, saltcon=0.150,
/
mmpbsa.in generated with --create_input gb
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Input block generated for the 1.7.0 release.
Be careful with the variables you modify, some can have severe consequences on the results you obtain.

# General namelist variables
&general
  sys_name                       = "Stability"                       # System name; e.g. "complex"
  startframe                     = 1                                      # First frame; e.g. 1
  endframe                       = 10                                     # Last frame; e.g. 100
  interval                       = 1                                      # Frame interval; e.g. 1


  PBRadii                        = 4                                      # PB radii set; 1-7
  temperature                    = 298.15                                 # Temperature (K); e.g. 298.15
  qh_entropy                     = 0                                      # Legacy QH output reader; new calculations reject 1
  interaction_entropy            = 0                                      # Run IE entropy; 0/1
  ie_segment                     = 25                                     # IE tail diagnostic only (%); not primary IE; e.g. 25
  c2_entropy                     = 0                                      # Run C2 entropy; 0/1
  assign_chainID                 = 0                                      # Assign chain IDs; 0/1
  exp_ki                         = 0.0                                    # Experimental Ki (nM); e.g. 0.0
  full_traj                      = 0                                      # Write full trajectory; 0/1
  gmx_path                       = ""                                     # GROMACS path; e.g. "/usr/bin"
  keep_files                     = 2                                      # Files to keep; 0-2
  netcdf                         = 0                                      # Use NetCDF; 0/1
  solvated_trajectory            = 1                                      # Clean solvated traj.; 0/1
  explicit_waters                = 0                                      # Explicit waters; e.g. 10
  explicit_waters_mask           = "dASA"                                     # Water reference; e.g. ":1-10", "within 4", "dASA"
  explicit_waters_group          = "automatic"                                     # Solvent group; e.g. "TIP3" or "automatic"
  explicit_waters_dasa_cutoff    = 0.5                                    # dASA cutoff; e.g. 0.5
  explicit_waters_as             = "receptor"                             # Water owner; e.g. "receptor"
  explicit_waters_extra_points   = "error"                                # Virtual sites; "error" or "strip"
  verbose                        = 1                                      # Output verbosity; 0-2
/

# (AMBER) Generalized-Born namelist variables
&gb
  igb                            = 8                                      # GB model, e.g. 2 or 8
  intdiel                        = 1.0                                    # Internal dielectric; e.g. 1.0
  extdiel                        = 78.5                                   # External dielectric; e.g. 78.5
  saltcon                        = 0.150                                  # Salt conc. (M); e.g. 0.150
  surften                        = 0.0072                                 # Surface tension; e.g. 0.0072
  surfoff                        = 0.0                                    # Surface offset; e.g. 0.0
  molsurf                        = 0                                      # Use molsurf; 0/1
  msoffset                       = 0.0                                    # Molsurf offset; e.g. 0.0
  probe                          = 1.4                                    # Probe radius (A); e.g. 1.4
  ifqnt                          = 0                                      # Enable QM/MM; 0/1
  qm_theory                      = "PM6-DH+"                              # QM theory; e.g. "PM6-DH+"
  qm_residues                    = ""                                     # QM residues; e.g. ":1-5"
  com_qmmask                     = ""                                     # Complex QM mask; e.g. ":1-5"
  rec_qmmask                     = ""                                     # Receptor QM mask; e.g. ":1-5"
  lig_qmmask                     = ""                                     # Ligand QM mask; e.g. ":1"
  qmcharge_com                   = 0                                      # Complex QM charge; e.g. 0
  qmcharge_lig                   = 0                                      # Ligand QM charge; e.g. 0
  qmcharge_rec                   = 0                                      # Receptor QM charge; e.g. 0
  qmcut                          = 9999.0                                 # QM cutoff (A); e.g. 9999
  scfconv                        = 1e-08                                  # SCF convergence; e.g. 1.0e-8
  itrmax                         = 1000                                   # Maximum SCF iterations; e.g. 5000
  # ndiis_attempts                 = None                                 # Maximum DIIS attempts per SCF cycle; e.g. 700
  peptide_corr                   = 0                                      # Peptide correction; 0/1
  writepdb                       = 1                                      # Write QM PDB; 0/1
  verbosity                      = 0                                      # QM/MM verbosity; 0-5
  alpb                           = 0                                      # Use ALPB; 0/1
  arad_method                    = 1                                      # ALPB size method; e.g. 1
/

Keep in mind

This input provides a practical starting point and can serve as the basis for production calculations. Review the available input-file options, their accepted values, and adjust settings that depend on your system or protocol. Additional sample inputs are available here.

How this example works

The -s flag activates stability mode. gmx_MMPBSA evaluates only the selected complex and ignores any separately supplied receptor or ligand information. The source trajectory is solvated, but the SOLU_chain1 and SOLU_chain2 index groups select the 608-atom protein-protein solute for analysis.

The calculation processes frames 1 through 10 with GB-Neck2 (igb=8), the matching mbondi3 radii (PBRadii=4), and a salt concentration of 0.15 M.

Interpretation

Stability mode reports the molecular-mechanics and solvation energy of one selected system. It does not by itself calculate a binding free energy or an experimental folding free energy. Its results are most useful in a consistently prepared comparison, such as related structures or variants evaluated with the same protocol.

Expected outputs

A successful calculation produces:

  • FINAL_RESULTS_MMPBSA.dat: the single-system MM/GBSA energy summary and statistics.
  • FINAL_RESULTS_MMPBSA.csv: the per-frame energy terms requested with -eo.

Analyze the results

Open the results with gmx_MMPBSA_ana for interactive inspection and plotting. See the gmx_MMPBSA_ana documentation for usage details.

Last update: September 13, 2026 05:57:32
Created: October 17, 2020 22:44:10
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