Description

gplt is a very convenient python tool for plotting gromacs output file, such as .xvg, .xpm or convert .dat to .xpm for visualization. This tool is similar to DuIvyTools, and these features could potentially be part of DuIvyTools. However, if time permits, I hope that it can become more powerful than DuIvyTools in the future.

Cite

Attention

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

Yujie Liu, gplt. Zenodo. https://doi.org/10.5281/zenodo.13208831

Installation

  • Requirements

    • Python >= 3.8

    • numpy, matplotlib, openpyxl, etc.

  • Install

    The module is installed by pip method:

    pip install numpy matplotlib colorama pandas openpyxl
pip install gplt -i https://test.pypi.org/simple

    Please ALWAYS install Latest version.

    Update this module if you have installed:

    pip install gplt --upgrade -i https://test.pypi.org/simple

Usage

General options

Use -h to show available options:

gplt -h

Plot xvg

gplt -f rdf.xvg
gplt -f rdf.xvg -ux angstrom
rdf rdf2

Of course support multi-figures:

gplt -f rdf1.xvg rdf2.xvg -legend lab1 lab2
FES

Plot xpm

Free Energy Landscape

gplt -f gibbs.xpm
gplt -f gibbs.xpm -d3
FES FES3D

Protein Structure

gplt -f ss.xpm
ss

Hydrogen Bonds

If you provide three files: hbond.ndx and hbmap.xpm generated by gmx hbond and system .gro , the program can use Donor-Acceptor label (resname+resid@atomname) to replace yticks.

Note

The ndx file name must be placed before the gro/xpm file

gplt -f hbond.ndx 1EBZ.gro hbmap.xpm -yaxis 'Hbonds Pairs' -title ''
hbpairs

Note

You can change some plotting style by Matplotlib style. Write a plain text file style.mplstyle:

axes.labelsize:     8
axes.linewidth:     1
xtick.labelsize:    8
ytick.labelsize:    8
ytick.left:         True
ytick.direction:    in
xtick.bottom:       True
xtick.direction:    in
lines.linewidth:    1.5
legend.fontsize:    8
legend.loc:         best
font.family:        Times New Roman
font.size:          8

Then add -style style.mplstyle option to gplt command line

Plot dat

Some plain text with .dat file extension

  1. .dat from gmx densmap -od

gplt -f densmap.dat && gplt -f densmap.xpm -aspect equal

This command will generate a densmap.xpm file, then you can plot it.

-aspect equal: Use same scaling from data to plot units for x and y

image-20250730104824434

  1. dssp.dat from gmx dssp (gmx >= 2023)

    gplt -f dssp.dat && gplt -f dssp.xpm -xprec 0 -yprec 0 -o dssp.png && gplt -f scount.xvg -xprec 0 -yprec 0 -o scount.png
dssp scount

  1. .dat with xyz columns

    gplt also supports the file with three columns xbin ybin zvalue, such as:

    1 14 0.0771830985915493
4 14 0.0771830985915493
7 14 0.0876056338028169
4 16 0.03492957746478873
6 13 0.011830985915492958
9 14 0.07887323943661971
16 14 0.08647887323943662
12 17 0.05718309859154929
13 14 0.07549295774647888

    x and y of grid point must be integer.

    gplt -f xyz.dat && gplt -f xyz.xpm -aspect equal
    xyz