MDanalysis/Nucleosome_dimer_MD_preparation.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Required\n",
    "* forcefield\n",
    "* initial pdb\n",
    "* installed gromacs\n",
    "* installed MDAnalysis"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [],
   "source": [
    "import MDAnalysis as mda\n",
    "from MDAnalysis.analysis import align\n",
    "from MDAnalysis.analysis.rms import rmsd\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "#### Trimming h2a and h2b as it was performed in [JMB](https://linkinghub.elsevier.com/retrieve/pii/S0022283615006956)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stderr",
     "output_type": "stream",
     "text": [
      "/home/armeev/miniconda3/envs/mdanalysis/lib/python3.6/site-packages/MDAnalysis/topology/guessers.py:72: UserWarning: Failed to guess the mass for the following atom types: MN\n",
      "  warnings.warn(\"Failed to guess the mass for the following atom types: {}\".format(atom_type))\n"
     ]
    }
   ],
   "source": [
    "nucl=mda.Universe(\"1kx5.pdb\")\n",
    "dimer=nucl.select_atoms(\"(segid C and resid 12:119) or (segid D and resid 26:200 )\")\n",
    "dimer.write(\"h2a_h2b_tr.pdb\")"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Performing PDB2GMX"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash  --out out --err err\n",
    "source /usr/local/gromacs/bin/GMXRC\n",
    "mkdir GMX_system\n",
    "cd GMX_system\n",
    "ln -s ../charmm36-jul2017.ff/ .\n",
    "gmx pdb2gmx -f ../h2a_h2b_tr.pdb -o init.pdb -p topol.top \\\n",
    "-i posre.itp -water tip3p -ff charmm36-jul2017\n",
    "\n",
    "gmx editconf -bt cubic -d 2 -c -f init.pdb -o init_box.pdb"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Out:\n",
      " turning H bonds into constraints...\n",
      "turning H bonds into constraints...\n",
      "Analysing residue names:\n",
      "There are:   205    Protein residues\n",
      "Analysing Protein...\n",
      "This run will generate roughly 0 Mb of data\n",
      "\n",
      "Err:\n",
      "                       :-) GROMACS - gmx grompp, 2018.3 (-:\n",
      "\n",
      "                            GROMACS is written by:\n",
      "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
      "    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  \n",
      "  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   \n",
      " Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    \n",
      "  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  \n",
      "  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   \n",
      "    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  \n",
      "   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen \n",
      " Christian Wennberg    Maarten Wolf   \n",
      "                           and the project leaders:\n",
      "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
      "\n",
      "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
      "Copyright (c) 2001-2017, The GROMACS development team at\n",
      "Uppsala University, Stockholm University and\n",
      "the Royal Institute of Technology, Sweden.\n",
      "check out http://www.gromacs.org for more information.\n",
      "\n",
      "GROMACS is free software; you can redistribute it and/or modify it\n",
      "under the terms of the GNU Lesser General Public License\n",
      "as published by the Free Software Foundation; either version 2.1\n",
      "of the License, or (at your option) any later version.\n",
      "\n",
      "GROMACS:      gmx grompp, version 2018.3\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/armeev/Projects/Modelling/MolModEdu/MDanalysis\n",
      "Command line:\n",
      "  gmx grompp -f Protocols/minimization.mdp -c GMX_system/init_box.pdb -p GMX_system/topol.top -o GMX_run/minimization.tpr -r GMX_system/init_box.pdb\n",
      "\n",
      "Setting the LD random seed to -667031372\n",
      "Generated 97877 of the 97903 non-bonded parameter combinations\n",
      "Generating 1-4 interactions: fudge = 1\n",
      "Generated 64492 of the 97903 1-4 parameter combinations\n",
      "Excluding 3 bonded neighbours molecule type 'Protein_chain_C'\n",
      "Excluding 3 bonded neighbours molecule type 'Protein_chain_D'\n",
      "\n",
      "NOTE 1 [file topol.top, line 47]:\n",
      "  System has non-zero total charge: 21.000000\n",
      "  Total charge should normally be an integer. See\n",
      "  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n",
      "  for discussion on how close it should be to an integer.\n",
      "  \n",
      "\n",
      "\n",
      "Removing all charge groups because cutoff-scheme=Verlet\n",
      "Number of degrees of freedom in T-Coupling group rest is 8197.00\n",
      "\n",
      "NOTE 2 [file Protocols/minimization.mdp]:\n",
      "  You are using a plain Coulomb cut-off, which might produce artifacts.\n",
      "  You might want to consider using PME electrostatics.\n",
      "\n",
      "\n",
      "\n",
      "There were 2 notes\n",
      "\n",
      "GROMACS reminds you: \"You Look Better Upside Down\" (Throwing Muses)\n",
      "\n",
      "                      :-) GROMACS - gmx mdrun, 2018.3 (-:\n",
      "\n",
      "                            GROMACS is written by:\n",
      "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
      "    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  \n",
      "  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   \n",
      " Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    \n",
      "  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  \n",
      "  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   \n",
      "    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  \n",
      "   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen \n",
      " Christian Wennberg    Maarten Wolf   \n",
      "                           and the project leaders:\n",
      "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
      "\n",
      "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
      "Copyright (c) 2001-2017, The GROMACS development team at\n",
      "Uppsala University, Stockholm University and\n",
      "the Royal Institute of Technology, Sweden.\n",
      "check out http://www.gromacs.org for more information.\n",
      "\n",
      "GROMACS is free software; you can redistribute it and/or modify it\n",
      "under the terms of the GNU Lesser General Public License\n",
      "as published by the Free Software Foundation; either version 2.1\n",
      "of the License, or (at your option) any later version.\n",
      "\n",
      "GROMACS:      gmx mdrun, version 2018.3\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/armeev/Projects/Modelling/MolModEdu/MDanalysis\n",
      "Command line:\n",
      "  gmx mdrun -deffnm GMX_run/minimization\n",
      "\n",
      "Reading file GMX_run/minimization.tpr, VERSION 2018.3 (single precision)\n",
      "Using 1 MPI thread\n",
      "Using 8 OpenMP threads \n",
      "\n",
      "\n",
      "Steepest Descents:\n",
      "   Tolerance (Fmax)   =  1.00000e+02\n",
      "   Number of steps    =         5000\n",
      "\n",
      "writing lowest energy coordinates.\n",
      "\n",
      "Steepest Descents converged to Fmax < 100 in 1677 steps\n",
      "Potential Energy  = -1.8213428e+04\n",
      "Maximum force     =  9.6151176e+01 on atom 2201\n",
      "Norm of force     =  8.3892308e+00\n",
      "\n",
      "GROMACS reminds you: \"Everybody has a plan until they get punched in the mouth\" (Mike Tyson)\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print('Out:\\n',out)\n",
    "print('Err:\\n',err)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash  --out out --err err\n",
    "source /usr/local/gromacs/bin/GMXRC\n",
    "mkdir GMX_run\n",
    "gmx grompp -f Protocols/minimization.mdp -c GMX_system/init_box.pdb -p GMX_system/topol.top \\\n",
    "-o GMX_run/minimization.tpr -r GMX_system/init_box.pdb\n",
    "gmx mdrun -deffnm GMX_run/minimization"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Out:\n",
      " turning H bonds into constraints...\n",
      "turning H bonds into constraints...\n",
      "Analysing residue names:\n",
      "There are:   205    Protein residues\n",
      "Analysing Protein...\n",
      "This run will generate roughly 0 Mb of data\n",
      "\n",
      "Err:\n",
      "                       :-) GROMACS - gmx grompp, 2018.3 (-:\n",
      "\n",
      "                            GROMACS is written by:\n",
      "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
      "    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  \n",
      "  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   \n",
      " Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    \n",
      "  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  \n",
      "  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   \n",
      "    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  \n",
      "   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen \n",
      " Christian Wennberg    Maarten Wolf   \n",
      "                           and the project leaders:\n",
      "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
      "\n",
      "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
      "Copyright (c) 2001-2017, The GROMACS development team at\n",
      "Uppsala University, Stockholm University and\n",
      "the Royal Institute of Technology, Sweden.\n",
      "check out http://www.gromacs.org for more information.\n",
      "\n",
      "GROMACS is free software; you can redistribute it and/or modify it\n",
      "under the terms of the GNU Lesser General Public License\n",
      "as published by the Free Software Foundation; either version 2.1\n",
      "of the License, or (at your option) any later version.\n",
      "\n",
      "GROMACS:      gmx grompp, version 2018.3\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/armeev/Projects/Modelling/MolModEdu/MDanalysis\n",
      "Command line:\n",
      "  gmx grompp -f Protocols/minimization.mdp -c GMX_system/init_box.pdb -p GMX_system/topol.top -o GMX_run/minimization.tpr -r GMX_system/init_box.pdb\n",
      "\n",
      "Setting the LD random seed to -667031372\n",
      "Generated 97877 of the 97903 non-bonded parameter combinations\n",
      "Generating 1-4 interactions: fudge = 1\n",
      "Generated 64492 of the 97903 1-4 parameter combinations\n",
      "Excluding 3 bonded neighbours molecule type 'Protein_chain_C'\n",
      "Excluding 3 bonded neighbours molecule type 'Protein_chain_D'\n",
      "\n",
      "NOTE 1 [file topol.top, line 47]:\n",
      "  System has non-zero total charge: 21.000000\n",
      "  Total charge should normally be an integer. See\n",
      "  http://www.gromacs.org/Documentation/Floating_Point_Arithmetic\n",
      "  for discussion on how close it should be to an integer.\n",
      "  \n",
      "\n",
      "\n",
      "Removing all charge groups because cutoff-scheme=Verlet\n",
      "Number of degrees of freedom in T-Coupling group rest is 8197.00\n",
      "\n",
      "NOTE 2 [file Protocols/minimization.mdp]:\n",
      "  You are using a plain Coulomb cut-off, which might produce artifacts.\n",
      "  You might want to consider using PME electrostatics.\n",
      "\n",
      "\n",
      "\n",
      "There were 2 notes\n",
      "\n",
      "GROMACS reminds you: \"You Look Better Upside Down\" (Throwing Muses)\n",
      "\n",
      "                      :-) GROMACS - gmx mdrun, 2018.3 (-:\n",
      "\n",
      "                            GROMACS is written by:\n",
      "     Emile Apol      Rossen Apostolov      Paul Bauer     Herman J.C. Berendsen\n",
      "    Par Bjelkmar    Aldert van Buuren   Rudi van Drunen     Anton Feenstra  \n",
      "  Gerrit Groenhof    Aleksei Iupinov   Christoph Junghans   Anca Hamuraru   \n",
      " Vincent Hindriksen Dimitrios Karkoulis    Peter Kasson        Jiri Kraus    \n",
      "  Carsten Kutzner      Per Larsson      Justin A. Lemkul    Viveca Lindahl  \n",
      "  Magnus Lundborg   Pieter Meulenhoff    Erik Marklund      Teemu Murtola   \n",
      "    Szilard Pall       Sander Pronk      Roland Schulz     Alexey Shvetsov  \n",
      "   Michael Shirts     Alfons Sijbers     Peter Tieleman    Teemu Virolainen \n",
      " Christian Wennberg    Maarten Wolf   \n",
      "                           and the project leaders:\n",
      "        Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel\n",
      "\n",
      "Copyright (c) 1991-2000, University of Groningen, The Netherlands.\n",
      "Copyright (c) 2001-2017, The GROMACS development team at\n",
      "Uppsala University, Stockholm University and\n",
      "the Royal Institute of Technology, Sweden.\n",
      "check out http://www.gromacs.org for more information.\n",
      "\n",
      "GROMACS is free software; you can redistribute it and/or modify it\n",
      "under the terms of the GNU Lesser General Public License\n",
      "as published by the Free Software Foundation; either version 2.1\n",
      "of the License, or (at your option) any later version.\n",
      "\n",
      "GROMACS:      gmx mdrun, version 2018.3\n",
      "Executable:   /usr/local/gromacs/bin/gmx\n",
      "Data prefix:  /usr/local/gromacs\n",
      "Working dir:  /home/armeev/Projects/Modelling/MolModEdu/MDanalysis\n",
      "Command line:\n",
      "  gmx mdrun -deffnm GMX_run/minimization\n",
      "\n",
      "Reading file GMX_run/minimization.tpr, VERSION 2018.3 (single precision)\n",
      "Using 1 MPI thread\n",
      "Using 8 OpenMP threads \n",
      "\n",
      "\n",
      "Steepest Descents:\n",
      "   Tolerance (Fmax)   =  1.00000e+02\n",
      "   Number of steps    =         5000\n",
      "\n",
      "writing lowest energy coordinates.\n",
      "\n",
      "Steepest Descents converged to Fmax < 100 in 1677 steps\n",
      "Potential Energy  = -1.8213428e+04\n",
      "Maximum force     =  9.6151176e+01 on atom 2201\n",
      "Norm of force     =  8.3892308e+00\n",
      "\n",
      "GROMACS reminds you: \"Everybody has a plan until they get punched in the mouth\" (Mike Tyson)\n",
      "\n",
      "\n"
     ]
    }
   ],
   "source": [
    "print('Out:\\n',out)\n",
    "print('Err:\\n',err)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash  --out out --err err\n",
    "source /usr/local/gromacs/bin/GMXRC\n",
    "gmx grompp -f Protocols/equilibration_vac.mdp -c GMX_run/minimization.gro -p GMX_system/topol.top \\\n",
    "-o GMX_run/equilibration.tpr -r GMX_system/init_box.pdb -v\n",
    "gmx mdrun -deffnm GMX_run/equilibration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print('Out:\\n',out)\n",
    "print('Err:\\n',err)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 62,
   "metadata": {},
   "outputs": [],
   "source": [
    "%%bash  --out out --err err\n",
    "source /usr/local/gromacs/bin/GMXRC\n",
    "gmx grompp -f Protocols/production_vac.mdp -c GMX_run/equilibration.gro -p GMX_system/topol.top \\\n",
    "-o GMX_run/production.tpr -t GMX_run/equilibration.cpt -r GMX_system/init_box.pdb -v\n",
    "gmx mdrun -deffnm GMX_run/production"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "print('Out:\\n',out)\n",
    "print('Err:\\n',err)"
   ]
  }
 ],
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