BioGem Blog

A simple Gnuplot script designed to generate a customized 2D line plot of potential energy data (presumably vs. simulation steps or time), using data from a file named PE.txt (available in GitHub ). The script applies several visual formatting settings to make the plot visually appealing and informative. This script produces a clean, stylized 2D plot of potential energy vs. simulation steps with (1) custom fonts, colors, and line styles, (2) no legend, (3) margins around the x-axis, and (4) automatic y-axis scaling. Source Code set title '{/Times-New-Roman=14:Bold Potential Energy Plot}' tc rgb '#167116' set xlabel '{/Arial:Italic Number of steps}' tc rgb 'red' set ylabel '{/Arial:Italic Potential energy}' tc rgb 'red' set style line 1 lt 1 lc rgb '#f70453' lw 0.5 set grid layerdefault lt 0 lc rgb 'blue' lw 0.5 set border lt 1 lc rgb 'blue' lw 1 unset key plot 'PE.txt' with lines ls 1 set xrang...

Intermolecular interactions are weak bonds formed due to electron sharing between two or more atoms to hold a molecule together. In molecular modelling or computer-aided drug designing (CADD), intermolecular interaction studies are performed to analyze the stability/energy of docking molecules. This video tutorial demonstrates two-dimensional (2D) plot and three-dimensional (3D) molecular visualization of protein-ligand and protein-protein inter-molecular interactions using LigPlot + /LigPlus tool. LigPlot + is a successor of original LigPlot program. The protein-ligand inter-molecular interactions are computed using LigPlot program and protein-protein or domain-domain inter-molecular interactions using DimPlot program. Moreover, the interactive 3D molecular visualization of the computed result can be viewed using RasMol or PyMOL. List of softwares used in this tutorial are LigPlot + , LigPlus , RasMol , PyMOL , and JDK .