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Normal-mode entropy calculations

This example estimates the entropic contribution to protein-protein binding with normal-mode analysis (NMODE). It combines a ten-frame MM/GBSA calculation using GB-Neck2 at 303.15 K with a frame-matched ten-frame NMODE demonstration.

  • Entropy method

    Normal-mode analysis

  • MM/GBSA model

    GB-Neck2 (igb=8)

  • NMODE frames

    Frames 1-10

  • Bundled test

    gmx_MMPBSA_test -t 17

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 any *.itp files referenced by the topology in the same directory.

  • Trajectory

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

  • Molecular selections

    Index index.ndx (-ci) and receptor/ligand group names or zero-based group numbers (-cg)

A complex reference structure without hydrogens may also be supplied with -cr. It is optional but recommended when you need specific chain IDs or residue numbering. 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 17

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

Run it manually

Download the NMODE example as a ZIP archive.

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

gmx_MMPBSA -O \
  -i mmpbsa.in \
  -cs com.tpr \
  -ct com_traj.xtc \
  -ci index.ndx \
  -cg 3 4 \
  -cp topol.top \
  -o FINAL_RESULTS_MMPBSA.dat \
  -eo FINAL_RESULTS_MMPBSA.csv

mpirun -np 2 gmx_MMPBSA -O \
  -i mmpbsa.in \
  -cs com.tpr \
  -ct com_traj.xtc \
  -ci index.ndx \
  -cg 3 4 \
  -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 nmode 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 MM/GBSA and NMODE calculation.

mmpbsa.in
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Sample input file for entropy calculations (nmode)
# This sample input is intended only to demonstrate that gmx_MMPBSA works.
# Although it follows the recommendations in the Amber manual, some parameters
# have been adjusted to keep the computational cost reasonable. Modify them as
# appropriate for your system.

&general
sys_name="NMode",
startframe=1,
endframe=10,
PBRadii=4,
temperature=303.15,
/
&gb
igb=8, saltcon=0.150,
/
# nmode processes the same ten frames selected in &general. The intentionally
# relaxed maxcyc and drms settings reduce the runtime and are not appropriate
# for a production calculation.
&nmode
nmstartframe=1,
nmendframe=10,
nminterval=1,
nmode_igb=1, nmode_istrng=0.150,
maxcyc=5, drms=2,
/
mmpbsa.in generated with --create_input gb nmode
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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                       = "NMode"                       # 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                    = 303.15                                 # 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
/

# Normal Modes Entropy namelist variables
&nmode
  nmstartframe                   = 1                                      # First NM frame; e.g. 1
  nmendframe                     = 10                                # Last NM frame; e.g. 100
  nminterval                     = 1                                      # NM frame stride; e.g. 1
  nmode_igb                      = 1                                      # GB model, e.g. 1
  nmode_istrng                   = 0.150                                    # NM ionic strength (M); e.g. 0.0
  dielc                          = 1.0                                    # NM dielectric; e.g. 1.0
  drms                           = 2                                  # Min. gradient cutoff; e.g. 0.001
  maxcyc                         = 5                                  # Max minimization cycles; e.g. 10000
/

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 single-trajectory approximation generates the receptor and ligand Amber-format topologies and trajectories from the complex. In this protein-protein system, the second protein is treated as the ligand. The command selects index groups 3 and 4 as the receptor and ligand, respectively.

The MM/GBSA calculation processes ten frames with GB-Neck2 (igb=8), the matching mbondi3 radii (PBRadii=4), a salt concentration of 0.15 M, and a temperature of 303.15 K. These settings now match the IE and C2 examples. NMODE also processes frames 1 through 10, giving a frame-matched ten-frame comparison.

The NMODE engine has a separate implicit-solvent control and supports only vacuum (nmode_igb=0) or its built-in HCT treatment (nmode_igb=1), not GB-Neck2. This example therefore retains nmode_igb=1 while matching the ionic strength at nmode_istrng=0.150 M.

Interpreting this demonstration

Warning

Normal-mode calculations are substantially more computationally expensive than IE or C2. This example sets maxcyc=5 and drms=2 solely to keep the bundled test short. These values provide much less minimization than the current defaults (maxcyc=10000, drms=0.001) and must not be treated as production-quality convergence settings.

For production work, use convergence criteria appropriate for the system and verify that the selected NMODE frames minimize successfully.

Expected outputs

A successful calculation produces:

  • FINAL_RESULTS_MMPBSA.dat: the MM/GBSA summary and NMODE entropy results.
  • FINAL_RESULTS_MMPBSA.csv: the per-frame energy and entropy 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: February 8, 2021 07:10:13
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