gmx_MMPBSA_test

`gmx_MMPBSA_test` command-line¶

$ gmx_MMPBSA_test -h
usage: gmx_MMPBSA_test [-h] [-v] 
       [-t [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,101,explicit_receptor_waters,gbnsr6,...} ...]]
       [-f FOLDER] [-r] [--examples-dir EXAMPLES_DIR] [--examples-source {clone,local}]
       [--skip-output-check] [-ng] [-n NUM_PROCESSORS] [-j NUM_CONCURRENT]

This program is part of gmx_MMPBSA and will allow you to run various gmx_MMPBSA examples easily.

optional arguments:
  -h, --help            show this help message and exit
  -v, --version         show program's version number and exit

Test options:
  -t [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,101} [{0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,101} ...]]
                        The level the test is going to be run at. Multiple systems and analysis can be run at the same 
                        time. Numeric ids, suite ids (`0`/`1`/`2`), legacy `101` (same as `0`), and named aliases
                        such as `explicit_receptor_waters` or `gbnsr6` are supported.
                              Nr. of Sys  
                        * 0      23     All -- Run all examples (Can take a long time!!!)
                        * 1      11     Minimal -- Does a minimal test with a set of systems and analyzes
                                        that show that gmx_MMPBSA runs correctly; slow or redundant cases
                                        are omitted from this suite
                        * 2       8     Fast -- Only the calculations that take a short time are run (Default)
                        [Systems]:
                             Slow Frames
                        * 3    . | 10   Protein-Ligand (Single trajectory approximation)
                        * 4    . | 10   Protein-Protein
                        * 5    . | 10   Protein-DNA
                        * 6    x |  4   Protein-Membrane CHARMM-GUI PROA-UQ2
                        * 7    . | 10   Protein-Glycan
                        * 8    x | 10  Metalloprotein-ligand
                        * 9    x | 10  Multicomponent system (Comp_receptor)
                        * 10   x |  4   Protein-Ligand (CHARMM force field)
                        * 11     |      Legacy alias for test 6 (consolidated membrane example)
                        [Analysis]:
                             Slow Frames
                        * 12   . | 10   Alanine Scanning
                        * 13   . | 10   Stability calculation
                        * 14   . | 10   Decomposition Analysis
                        * 15   . | 10  Interaction Entropy approximation
                        * 16   . | 10   Protein-Ligand (Multiple trajectory approximation)
                        * 17   x | 10  Entropy calculation using Normal Mode approximation
                        * 18   x |  4   Calculations using 3D-RISM approximation
                        * 19          C2 Entropy approximation
                        * 20          LPB Calculation
                        * 21          NLPB Calculation
                        * 22          Protein-Ligand_LPH (CHARMM force field)
                        * 23          QM/MMGBSA Calculation
                        * 24          GBNSR6 Calculation
                        * 25     |  5 AMBER input files
                        * 26     | 10 ST MM/PB(GB)SA with explicit receptor waters
  -f FOLDER, --folder FOLDER
                        Defines the folder to store all data
  -r, --reuse           Defines the existing test forlder will be reuse
  --examples-dir EXAMPLES_DIR
                        Use a local examples directory instead of cloning the repository
  --examples-source {clone,local}
                        Examples source mode. `local` requires `--examples-dir` or `GMXMMPBSA_TEST_EXAMPLES_DIR`
  --skip-output-check   Skip post-run verification of expected output files
  -ng, --nogui          No open gmx_MMPBSA_ana after all calculations finished
  -n NUM_PROCESSORS, --num_processors NUM_PROCESSORS
                        Defines the number of processor cores you want to use with MPI per calculation. If the number 
                        of frames is less than the number of cpus defined, the calculation will be performed with 
                        the number of processors = number of frames.
  -j NUM_CONCURRENT, --num_concurrent NUM_CONCURRENT
                        Defines the number of examples to run concurrently. Each example can use up to
                        --num_processors MPI ranks, so the total rank count can be -j * -n.


gmx_MMPBSA is an effort to implement the GB/PB and others calculations in GROMACS. 
Based on MMPBSA.py (version 16.0) and AmberTools20

Running gmx_MMPBSA_test¶

gmx_MMPBSA_test can run a predefined set of examples or an individual example. By default, examples run sequentially. To run multiple examples at the same time, use -j/--num_concurrent. Each example can use up to -n/--num_processors MPI ranks.

By default, gmx_MMPBSA_test clones the GitHub repository to obtain the examples/ folder. Developers working from a local checkout can point directly at that folder with --examples-dir (or the GMXMMPBSA_TEST_EXAMPLES_DIR environment variable) to avoid cloning and to test examples that match the installed code. After each successful run, the tool verifies that expected output files exist unless --skip-output-check is set.

Named selectors such as -t explicit_receptor_waters or -t gbnsr6 are equivalent to their numeric ids. -t 101 is a legacy alias for the full -t 0 suite. The former CHARMM membrane selector -t 11 is retained as a legacy alias for the consolidated membrane test 6; the full suite runs that example only once.

Sets in gmx_MMPBSA_test

Local examples (development)Named selectorFastParallel examplesMinimalAllMultiple selectionSingle selectionExplicit receptor watersAMBER input files

TMP_EXAMPLES=$(mktemp -d)
cp -a ./examples/. "$TMP_EXAMPLES/"
gmx_MMPBSA_test -f /tmp/gmx_test --examples-dir "$TMP_EXAMPLES" -t 2 -ng