gromacs package

Submodules

gromacs.gmx_order module

Module containing the GROMACS order class and the command line interface.

class gromacs.gmx_order.GMXOrder(input_top_path, input_traj_path, input_index_path=None, output_deuter_path=None, output_order_path=None, properties=None, **kwargs)

Bases: BiobbObject

biobb_mem GMXOrder

Wrapper of the GROMACS order module for computing lipid order parameters per atom for carbon tails.

GROMCAS order only works for saturated carbons and united atom force fields.

Parameters:

• input_top_path (str) – Path to the input structure or topology file. File type: input. Sample file. Accepted formats: tpr (edam:format_2333).

• input_traj_path (str) –

  Path to the input trajectory to be processed. File type: input. Sample file. Accepted formats: xtc (edam:format_3875), trr (edam:format_3910), cpt (edam:format_2333), gro (edam:format_2033), g96 (edam:format_2033), pdb (edam:format_1476), tng (edam:format_3876)..

• input_index_path (str) – Path to the GROMACS index file. File type: input. `Sample file <https://github.com/bioexcel/biobb_mem/raw/main/biobb_mem/test/data/ >`_. Accepted formats: ndx (edam:format_2033).

• output_deuter_path (str) –

  Path to deuterium order parameters xvgr/xmgr file. File type: output. Sample file. Accepted formats: xvg (edam:format_2330).

• output_order_path (str) (Optional) –

  Path to order tensor diagonal elements xvgr/xmgr file. File type: output. Sample file. Accepted formats: xvg (edam:format_2330).

• properties (dic - Python dictionary object containing the tool parameters, not input/output files) –

  • d (str) - (“z”) Direction of the normal on the membrane: z, x, y.

  • binary_path (str) - (“cpptraj”) Path to the cpptraj executable binary.

  • remove_tmp (bool) - (True) [WF property] Remove temporal files.

  • restart (bool) - (False) [WF property] Do not execute if output files exist.

  • sandbox_path (str) - (“./”) [WF property] Parent path to the sandbox directory.

Examples

This is a use example of how to use the building block from Python:

from biobb_mem.ambertools.gmx_order import gmx_order
prop = {
    'd': 'z'
}
gmx_order(input_top_path='/path/to/myTopology.top',
          input_traj_path='/path/to/myTrajectory.xtc',
          output_deuter_path='/path/to/deuterAnalysis.xvg',
          output_order_path='/path/to/orderAnalysis.xvg',
          properties=prop)

Info:

• wrapped_software:

  • name: GROMACS order

  • version: 2024.2

  • license: LGPL 2.1

• ontology:

  • name: EDAM

  • schema: http://edamontology.org/EDAM.owl

launch() → int

Execute the GMXOrder gromacs.gmx_order.GMXOrder object.

gromacs.gmx_order.gmx_order(input_top_path: str, input_traj_path: str, input_index_path: str | None = None, output_deuter_path: str | None = None, output_order_path: str | None = None, properties: dict | None = None, **kwargs) → int

Create GMXOrder class and execute launch() method

gromacs.gmx_order.main()

Command line execution of this building block. Please check the command line documentation.