updated codes

1aki/auto_md_230504.ipynb

@@ -0,0 +1,177 @@
+{
+ "cells": [
+  {
+   "attachments": {},
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# AUTO MD"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "'/mnt/c/Users/paul/works/1aki/1aki_2'"
+      ]
+     },
+     "execution_count": 1,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "pwd"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! gmx"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "! wget -O ions.mdp https://raw.githubusercontent.com/paulshamrat/ColabMDA/main/mdps/ions.mdp\n",
+    "! wget -O md.mdp https://raw.githubusercontent.com/paulshamrat/ColabMDA/main/mdps/md.mdp\n",
+    "! wget -O minim.mdp https://raw.githubusercontent.com/paulshamrat/ColabMDA/main/mdps/minim.mdp\n",
+    "! wget -O npt.mdp https://raw.githubusercontent.com/paulshamrat/ColabMDA/main/mdps/npt.mdp\n",
+    "! wget -O nvt.mdp https://raw.githubusercontent.com/paulshamrat/ColabMDA/main/mdps/nvt.mdp\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "\n",
+    "# Download pdb structure\n",
+    "! wget https://files.rcsb.org/download/1AKI.pdb\n",
+    "\n",
+    "# Strip out Water\n",
+    "! grep -v HOH 1AKI.pdb > 1AKI_clean.pdb\n",
+    "\n",
+    "# cleaned file\n",
+    "! gmx pdb2gmx -f 1AKI_clean.pdb -o 1AKI_processed.gro -water spce -ignh -ff amber99sb-ildn\n",
+    "\n",
+    "# add box\n",
+    "! gmx editconf -f 1AKI_processed.gro -o 1AKI_newbox.gro -c -d 1.0 -bt cubic\n",
+    "\n",
+    "# solvate\n",
+    "! gmx solvate -cp 1AKI_newbox.gro -cs spc216.gro -o 1AKI_solv.gro -p topol.top\n",
+    "\n",
+    "# final sove\n",
+    "! gmx grompp -f ions.mdp -c 1AKI_solv.gro -p topol.top -o ions.tpr\n",
+    "\n",
+    "\n",
+    "#This is a trick to provide interactive options to gmx\n",
+    "! echo \"SOL\" > options\n",
+    "! echo \" \" >> options\n",
+    "# Now we have an atomic-level description of our system in the binary file ions.tpr. We will pass this file to genion:\n",
+    "# When prompted, choose group 13 \"SOL\" for embedding ions.\n",
+    "! gmx genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -neutral < options\n",
+    "\n",
+    "\n",
+    "# Assemble the binary input using grompp using [](this) input parameter file:\n",
+    "! gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr\n",
+    "\n",
+    "#Using grompp to prepare our minimization MD\n",
+    "! gmx grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr\n",
+    "\n",
+    "#Run our minimization\n",
+    "! gmx mdrun -v -deffnm em\n",
+    "\n",
+    "\n",
+    "#This is a trick to provide interactive options to gmx\n",
+    "! echo \"Potential\" > options\n",
+    "! echo \" \" >> options\n",
+    "\n",
+    "# Let's do a bit of analysis. The em.edr file contains all of the energy terms that GROMACS collects during EM. \n",
+    "# You can analyze any .edr file using the GROMACS energy module:\n",
+    "! gmx energy -f em.edr -o potential.xvg < options\n",
+    "# At the prompt, type \"10 0\" to select Potential (10); zero (0) terminates input.\n",
+    "\n",
+    "\n",
+    "# We will call grompp and mdrun just as we did at the EM step:\n",
+    "! gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr\n",
+    "! gmx mdrun -deffnm nvt\n",
+    "\n",
+    "#################################\n",
+    "\n",
+    "\n",
+    "#This is a trick to provide interactive options to gmx\n",
+    "! echo \"Temperature\" > options\n",
+    "! echo \" \" >> options\n",
+    "# Let's analyze the temperature progression, again using energy:\n",
+    "! gmx energy -f nvt.edr -o temperature.xvg < options\n",
+    "# Type \"16 0\" at the prompt to select the temperature of the system and exit.\n",
+    "\n",
+    "\n",
+    "# We will call grompp and mdrun just as we did for NVT equilibration. \n",
+    "! gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr\n",
+    "! gmx mdrun -deffnm npt\n",
+    "\n",
+    "\n",
+    "\n",
+    "#This is a trick to provide interactive options to gmx\n",
+    "! echo \"Pressure\" > options\n",
+    "! echo \" \" >> options\n",
+    "# Let's analyze the pressure progression, again using energy:\n",
+    "! gmx energy -f npt.edr -o pressure.xvg < options\n",
+    "# Type \"18 0\" at the prompt to select the pressure of the system and exit. \n",
+    "\n",
+    "\n",
+    "\n",
+    "#This is a trick to provide interactive options to gmx\n",
+    "! echo \"Density\" > options\n",
+    "! echo \" \" >> options\n",
+    "\n",
+    "# Let's take a look at density as well\n",
+    "! gmx energy -f npt.edr -o density.xvg < options\n",
+    "# this time using energy and entering \"24 0\" at the prompt.\n",
+    "\n",
+    "\n",
+    "# We will run a 1-ns MD simulation,\n",
+    "! gmx grompp -f md.mdp -c npt.gro -t npt.cpt -p topol.top -o md_0_1.tpr\n",
+    "\n",
+    "\n",
+    "# Assuming you have one GPU available, the mdrun command to make use of it is as simple as:\n",
+    "! gmx mdrun -deffnm md_0_1"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.6"
+  },
+  "orig_nbformat": 4
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

1aki/density.xvg

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+# This file was created Thu May  4 15:06:59 2023
+# Created by:
+#              :-) GROMACS - gmx energy, 2021.4-Ubuntu-2021.4-2 (-:
+# 
+# Executable:   /bin/gmx
+# Data prefix:  /usr
+# Working dir:  /mnt/c/Users/paul/works/1aki/1aki_2
+# Command line:
+#   gmx energy -f npt.edr -o density.xvg
+# gmx energy is part of G R O M A C S:
+#
+# GROup of MAchos and Cynical Suckers
+#
+@    title "GROMACS Energies"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "(kg/m^3)"
+@TYPE xy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ s0 legend "Density"
+    0.000000  994.001953
+    1.000000  1019.782715
+    2.000000  1016.534729
+    3.000000  1014.574158
+    4.000000  1020.538635
+    5.000000  1019.669861
+    6.000000  1017.436218
+    7.000000  1021.530579
+    8.000000  1019.994568
+    9.000000  1017.937988
+   10.000000  1013.635864