TprParser 0.1.45

A reader of gromacs tpr file

Description

TprParser is a convenient Python module for reading and setting simulation parameters in gromacs tpr file.

This module mainly aimed to modify atom property of tpr and create a new tpr file (named new.tpr) after use any one set_ method.

The module only supports get atoms coordinates, velocity and force if exist in tpr by module.get_xvf(...) function.

However, many properties can be set up by module, such as total simulation time nsteps, simulation integrator interval dt, output control parameters (nstxout, nstvout, etc.) and temperature/pressure coupling parameters.

Compatibility

GROMACS tpr version should between 4.0 to 2024, too old tpr can not be read by this module.

Install

• Requirements

  • Python >= 3.8

  • Numpy

  • C++ compiler (g++ for Linux, MSVC for Windows)

• Install

  The module is installed by pip method:

  pip install TprParser -i https://pypi.org/simple
  

  Please ALWAYS install Latest version.

Usage

Write your python program like this:

from TprParser.TprReader import TprReader	# import this module

Get atom property

# get atom coords or velocity
reader = TprReader("your.tpr")
coords = reader.get_xvf('x')
velocity = reader.get_xvf('v')
# ...

Modify atom property

newcoords = np.array([[1,2,3], [4,5,6], [...]], dtype=np.float32) # shape= N*3
# The step will create new.tpr that used newcoords
reader.set_xvf('x', newcoords)

Modify system pressure

you can define a function do this work:

def Pressure(fname):
    reader = TprReader(fname)
    # 100 bar
    ref_p = [
        100, 0, 0,
        0, 100, 0,
        0, 0, 100
    ]
    # compressibility 4.5E-5
    compress = [
        4.5E-5, 0, 0,
        0, 4.5E-5, 0,
        0, 0, 4.5E-5
    ]
    assert len(ref_p) == 9
    assert len(compress) == 9
    # use ParrinelloRahman algorithm and Isotropic pressure coupling method
    reader.set_pressure('ParrinelloRahman', 'Isotropic', 1.0, ref_p, compress)

Other

Please see TprReader module annotation

Cite

If TprParser is utilized in your work, please cite as follows in main text:

Yujie Liu, TprParser, Version xxx, https://pypi.org/project/TprParser/

TODO

• More parameters can be modified
• Get More essential parameters