import subprocessimport osimport tempfileimport matplotlib.pyplot as plt# Define the protein PDB fileprotein$\_$file $="/$Users$/$shreyyadav$/$Downloads$/$group$\_14\_$biop$\_$SHREY$\_$YADAV$\_2022483,$ SOURABH$\_2022507,$ MD$\_$KAIF$\_2022289,$ BHASKAR KASHYAP$\_2022137,$ SATKEERAT SINGH KHOKHAR $2022459/$all$\_$pdb$\_$files$/7$l$6$k$.$pdb$"$# Define MDP files with updated pathsmdp$\_$files $=["$em$.$mdp$","$nvt$.$mdp$","$npt$.$mdp$","$md$.$mdp$"]$# GROMACS executable pathgmx$\_$path $="/$Users$/$shreyyadav$/$Downloads$/$gromacs$\_$install$/$bin$/$gmx$"$# Function to set up GROMACS environmentdef setup$\_$gmx$\_$environment$()$: try: subprocess.run$([$gmx$\_$path, $"--$version"$],$ check$=$True$)$ except FileNotFoundError: print$("$GROMACS not found in the system."$)$ raise except subprocess.CalledProcessError: print$("$GROMACS command failed to run."$)$ raise# Function to run MD simulation for a single proteindef run$\_$simulation$($protein$\_$file$)$: try: # Ensure GROMACS environment is set up setup$\_$gmx$\_$environment$()$ # Create a temporary directory for the simulation with tempfile.TemporaryDirectory$()$ as tmpdir: print$($f$"$Working in directory: $\{$tmpdir$\}")$ os$.$chdir$($tmpdir$)$ # Convert PDB to GROMACS format subprocess.run$([$gmx$\_$path, $"$pdb$2$gmx$","-$f$",$ protein$\_$file, $"-$o$",$ "processed.gro", $"-$water", "tip$3$p$"],$ check$=$True$)$ # Define box and add water subprocess.run$([$gmx$\_$path, "editconf", $"-$f$",$ "processed.gro", $"-$o$",$ "box.gro", $"-$c$","-$d$","1\mathrm{.}0","-$bt$",$ "cubic"$],$ check$=$True$)$ subprocess.run$([$gmx$\_$path, "solvate", $"-$cp$",$ "box.gro", $"-$cs$","$spc$216.$gro", $"-$o$",$ "solvated.gro", $"-$p$",$ "topol.top"$],$ check$=$True$)$ # Add ions subprocess.run$([$gmx$\_$path, "grompp", $"-$f$",$ mdp$\_$files$[0],"-$c$",$ "solvated.gro", $"-$p$",$ "topol.top", $"-$o$",$ "ions.tpr$"],$ check$=$True$)$ subprocess.run$([$gmx$\_$path, "genion", $"-$s$",$ "ions.tpr$","-$o$",$ "neutralized.gro", $"-$p$",$ "topol.top", $"-$pname", $"$NA$","-$nname", $"$CL$","-$neutral"$],$ check$=$True$)$ # Energy minimization subprocess.run$([$gmx$\_$path, "grompp", $"-$f$",$ mdp$\_$files$[0],"-$c$",$ "neutralized.gro", $"-$p$",$ "topol.top", $"-$o$","$em$.$tpr$"],$ check$=$True$)$ subprocess.run$([$gmx$\_$path, "mdrun", $"-$v$","-$deffnm", $"$em$"],$ check$=$True$)$ # NVT equilibration subprocess.run$([$gmx$\_$path, "grompp", $"-$f$",$ mdp$\_$files$[1],"-$c$","$em$.$gro", $"-$r$","$em$.$gro", $"-$p$",$ "topol.top", $"-$o$","$nvt$.$tpr$"],$ check$=$True$)$ subprocess.run$([$gmx$\_$path, "mdrun", $"-$v$","-$deffnm", $"$nvt$"],$ check$=$True$)$ # NPT equilibration subprocess.run$([$gmx$\_$path, "grompp", $"-$f$",$ mdp$\_$files$[2],"-$c$","$nvt$.$gro", $"-$r$","$nvt$.$gro", $"-$p$",$ "topol.top", $"-$o$","$npt$.$tpr$"],$ check$=$True$)$ subprocess.run$([$gmx$\_$path, "mdrun", $"-$v$","-$deffnm", $"$npt$"],$ check$=$True$)$ # $1$ns Production MD simulation subprocess.run$([$gmx$\_$path, "grompp", $"-$f$",$ mdp$\_$files$[3],"-$c$","$npt$.$gro", $"-$r$","$npt$.$gro", $"-$p$",$ "topol.top", $"-$o$","$md$.$tpr$"],$ check$=$True$)$ subprocess.run$([$gmx$\_$path, "mdrun", $"-$v$","-$deffnm", $"$md$"],$ check$=$True$)$ # Analysis of the results analyze$\_$results$($tmpdir$)$ except Exception as e: print$($f$"$Error running simulation for $\{$protein$\_$file$\}$: $\{$e$\}")$ os$.$chdir$("..")$# Function to analyze the results and generate the required plotsdef analyze$\_$results$($work$\_$dir$)$: os$.$chdir$($work$\_$dir$)$ # Energy Minimization Plot subprocess.run$([$gmx$\_$path, "energy", $"-$f$","$em$.$edr", $"-$o$","$em$\_$energy.xvg$"],$ input$=$"Potential

$",$ text$=$True, check$=$True$)$ # Plot RMSD $($Root Mean Square Deviation$)$ of protein backbone subprocess.run$([$gmx$\_$path, $"$rms$","-$s$","$md$.$tpr$","-$f$","$md$.$xtc$","-$o$","$rmsd$.$xvg$","-$tu$","$ns$"],$ input$="4$

$4$

$",$ text$=$True, check$=$True$)$ # Plot Radius of Gyration $($Rg$)$ subprocess.run$([$gmx$\_$path, "gyrate", $"-$s$","$md$.$tpr$","-$f$","$md$.$xtc$","-$o$","$rg$.$xvg$"],$ check$=$True$)$ # Plot Temperature, Pressure, and Density subprocess.run$([$gmx$\_$path, "energy", $"-$f$","$md$.$edr", $"-$o$",$ "temperature.xvg$"],$ input$=$"Temperature

$",$ text$=$True, check$=$True$)$ subprocess.run$([$gmx$\_$path, "energy", $"-$f$","$md$.$edr", $"-$o$",$ "pressure.xvg$"],$ input$=$"Pressure

$",$ text$=$True, check$=$True$)$ subprocess.run$([$gmx$\_$path, "energy", $"-$f$","$md$.$edr", $"-$o$",$ "density.xvg$"],$ input$=$"Density

$",$ text$=$True, check$=$True$)$ # Plotting the data plot$\_$data$()$ os$.$chdir$("..")$# Function to plot the graphsdef plot$\_$data$()$: # Plot RMSD plt$.$figure$()$ data $=$ read$\_$xvg$\_$file$("$rmsd$.$xvg$")$ plt$.$plot$($data$[0],$ data$[1])$ plt$.$xlabel$(\text{'}$Time $($ns$)\text{'})$ plt$.$ylabel$(\text{'}$RMSD $($nm$)\text{'})$ plt$.$title$(\text{'}$RMSD of Protein Backbone'$)$ plt$.$savefig$(\text{'}$rmsd$\_$plot.png$\text{'})$ # Plot Rg $($Radius of Gyration$)$ plt$.$figure$()$ data $=$ read$\_$xvg$\_$file$("$rg$.$xvg$")$ plt$.$plot$($data$[0],$ data$[1])$ plt$.$xlabel$(\text{'}$Time $($ns$)\text{'})$ plt$.$ylabel$(\text{'}$Rg $($nm$)\text{'})$ plt$.$title$(\text{'}$Radius of Gyration $($Rg$)\text{'})$ plt$.$savefig$(\text{'}$rg$\_$plot.png$\text{'})$ # Plot Temperature plt$.$figure$()$ data $=$ read$\_$xvg$\_$file$("$temperature$.$xvg$")$ plt$.$plot$($data$[0],$ data$[1])$ plt$.$xlabel$(\text{'}$Time $($ns$)\text{'})$ plt$.$ylabel$(\text{'}$Temperature $($K$)\text{'})$ plt$.$title$(\text{'}$Temperature Fluctuations'$)$ plt$.$savefig$(\text{'}$temperature$\_$plot.png$\text{'})$ # Plot Pressure plt$.$figure$()$ data $=$ read$\_$xvg$\_$file$("$pressure$.$xvg$")$ plt$.$plot$($data$[0],$ data$[1])$ plt$.$xlabel$(\text{'}$Time $($ns$)\text{'})$ plt$.$ylabel$(\text{'}$Pressure $($bar$)\text{'})$ plt$.$title$(\text{'}$Pressure Fluctuations'$)$ plt$.$savefig$(\text{'}$pressure$\_$plot.png$\text{'})$ # Plot Density plt$.$figure$()$ data $=$ read$\_$xvg$\_$file$("$density$.$xvg$")$ plt$.$plot$($data$[0],$ data$[1])$ plt$.$xlabel$(\text{'}$Time $($ns$)\text{'})$ plt$.$ylabel$(\text{'}$Density $($kg$/$m$^3)\text{'})$ plt$.$title$(\text{'}$Density Fluctuations'$)$ plt$.$savefig$(\text{'}$density$\_$plot.png$\text{'})$ plt$.$show$()$# Helper function to read $.$xvg data filesdef read$\_$xvg$\_$file$($filename$)$: x$,$ y $=[],[]$ with open$($filename$,\text{'}$r$\text{'})$ as f: for line in f: if not line.startswith$(("$#$","$@$"))$: columns $=$ line.split$()$ x$.$append$($float$($columns$[0]))$ y$.$append$($float$($columns$[1]))$ return x$,$ y# Run simulation for the given protein filerun$\_$simulation$($protein$\_$file$)$ please help me reduce the runtime for this code