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Running gmx_MMPBSA_ana

Running gmx_MMPBSA_ana

In order to analyze multiple systems in the same section and implement the correlation between them, we improved the file input to gmx_MMPBSA_ana. Currently, gmx_MMPBSA_ana supports either several info files, a folder that contains the info file, or a list of folders containing info files.

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

Here all folders (5 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 systems (4) 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 estructure only work if recursive option was defined. See the examples below

Note that:

  • System-1 is defined as folder that contain a _GMXMMPBSA_info
  • Folder-1 contain two folder (Systems), each containing a _GMXMMPBSA_info
  • System-3 is defined as a _GMXMMPBSA_info file

Here only 4 (systems) folders will be processed by gmx_MMPBSA_ana. The systems in the 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

  • other location Version: 1.4.0

    gmx_MMPBSA_ana -f /path/to/_GMXMMPBSA_info

Version: 1.4.0

Passing a folder as input:

  • Current directory

    gmx_MMPBSA_ana -f .

  • other location

    gmx_MMPBSA_ana -f /path/to/folder

Remember

This folder must contain a valid _GMXMMPBSA_info file

Version: 1.4.0

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

Version: 1.4.0

Passing a folder as input with recursive option:

  • Current directory

    gmx_MMPBSA_ana -f . -r

  • other 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
    • Note that if you remove the option -r, each folder must contain a valid _GMXMMPBSA_info file.
Last update: January 27, 2022 07:53:46
Created: January 27, 2022 07:53:46
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