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Running gmx_MMPBSA_ana

Running gmx_MMPBSA_ana

To analyze multiple systems in the same session or calculate correlations between them, you can supply several info files, a folder containing an info file, or a list of folders containing info files to gmx_MMPBSA_ana.

Current result summaries

Current results can expose frame-based SD/SEM and deterministic block-based Block SD/Block SEM values. Block SEM is the recommended uncertainty representation when at least two complete blocks are available; it does not establish convergence or block independence. The analyzer keeps the legacy fields for compatibility.

Correlation systems

The bundled correlation example contains one wild-type system and six mutant-only systems. Frames from different systems are not paired automatically, so interpret correlations from the resulting system summaries rather than assuming frame-by-frame correspondence.

Make sure to use the following structure when working with several folders:

Here, all five systems will be processed by gmx_MMPBSA_ana: 

Defined folder
  ├── System-1
  │      └── _GMXMMPBSA_info
  ├── System-2
  │      └── _GMXMMPBSA_info
  ├── System-3
  │      └── _GMXMMPBSA_info
  ├── System-4
  │      └── _GMXMMPBSA_info
  └── System-5
         └── _GMXMMPBSA_info

Here, all four systems will be processed by gmx_MMPBSA_ana: 

System-1      
  └──_GMXMMPBSA_info
Folder-1
  ├── System-2.1
  │      └── _GMXMMPBSA_info
  └── System-2.2
         └── _GMXMMPBSA_info
System-3 (_GMXMMPBSA_info)

The command-line for this is:

gmx_MMPBSA_ana -f /path/to/System-1 /path/to/System-3/_GMXMMPBSA_info /path/to/Folder-1 -r

This structure works only when the recursive option is enabled. See the examples below.

Note that:

  • System-1 is a folder containing a _GMXMMPBSA_info file
  • Folder-1 contains two system folders, each containing a _GMXMMPBSA_info file
  • System-3 is defined as a _GMXMMPBSA_info file

Here, only four system folders will be processed by gmx_MMPBSA_ana. The systems in Internal folder will be ignored: 

Defined folder
  ├── System-1
  │      └── _GMXMMPBSA_info
  ├── System-2
  │      └── _GMXMMPBSA_info
  ├── Internal folder
  │      ├─X─ System-3.1
  │      │      └── _GMXMMPBSA_info
  │      └─X─ System-3.2
  │             └── _GMXMMPBSA_info
  ├── System-4
  │      └── _GMXMMPBSA_info
  └── System-5
         └── _GMXMMPBSA_info

Examples

Passing a _GMXMMPBSA_info file as input:

  • Current directory

    gmx_MMPBSA_ana -f _GMXMMPBSA_info

  • Another location

    gmx_MMPBSA_ana -f /path/to/_GMXMMPBSA_info

Passing a folder as input:

  • Current directory

    gmx_MMPBSA_ana -f .

  • Another location

    gmx_MMPBSA_ana -f /path/to/folder

Remember

This folder must contain a valid _GMXMMPBSA_info file

gmx_MMPBSA_ana -f /path/to/folder-1 /path/to/_GMXMMPBSA_info-1 /path/to/folder-2

Remember

  • All defined folders must contain a valid _GMXMMPBSA_info file
  • All _GMXMMPBSA_info files defined must be valid

Passing a folder as input with the recursive option:

  • Current directory

    gmx_MMPBSA_ana -f . -r

  • Another location

    gmx_MMPBSA_ana -f /path/to/folder --recursive

  • Combine multiple folders

    gmx_MMPBSA_ana -f /path/to/folder-1 /path/to/folder-2 /path/to/folder-3  -r

    Folders can contain one or more systems

  • Combine multiple folders and files

    gmx_MMPBSA_ana -f /path/to/folder-1 /path/to/_GMXMMPBSA_info-1 /path/to/folder-3  -r
    • Folders can contain one or more systems
    • If you remove -r, each folder must contain a valid _GMXMMPBSA_info file.
Last update: September 10, 2026 04:34:05
Created: January 27, 2022 07:53:46
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