5_trj_preprocessing.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Trajectory preprocessing"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We need to make molecules whole and center them\n",
    "http://www.gromacs.org/Documentation/Terminology/Periodic_Boundary_Conditions\n",
    "http://manual.gromacs.org/documentation/current/onlinehelp/gmx-trjconv.html"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "text/markdown": [
       "\n",
       "# MD simulations of H3-H4 with 30 bp of DNA, tails truncated\n",
       "- AMBER14SB force field\n",
       "- 150 mM NaCl\n",
       "- box 2nm\n"
      ],
      "text/plain": [
       "<IPython.core.display.Markdown object>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "#Reloading funcs if changed\n",
    "from importlib import reload \n",
    "import funcs,config\n",
    "reload(funcs)\n",
    "reload(config)\n",
    "\n",
    "\n",
    "from IPython.display import Markdown, display\n",
    "from config import folder,descr,pname\n",
    "display(Markdown(descr))\n"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "gmx: Relink `/opt/miniconda3/envs/moldyn/bin/../lib/././libgfortran.so.4' with `/lib/x86_64-linux-gnu/librt.so.1' for IFUNC symbol `clock_gettime'\n",
      "                     :-) GROMACS - gmx trjconv, 2018.4 (-:\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 trjconv, version 2018.4\n",
      "Executable:   /opt/miniconda3/envs/moldyn/bin/gmx\n",
      "Data prefix:  /opt/miniconda3/envs/moldyn\n",
      "Working dir:  /home/_shared/_projects/gmx_template\n",
      "Command line:\n",
      "  gmx trjconv -n GMX_system/index.ndx -f GMX_run/7_prod.xtc -s GMX_run/7_prod.tpr -o tmp/7_prod_1.xtc -pbc whole\n",
      "\n",
      "Will write xtc: Compressed trajectory (portable xdr format): xtc\n",
      "Reading file GMX_run/7_prod.tpr, VERSION 2018.4 (single precision)\n",
      "Reading file GMX_run/7_prod.tpr, VERSION 2018.4 (single precision)\n",
      "Select group for output\n",
      "Group     0 (         System) has 169387 elements\n",
      "Group     1 (            DNA) has  1903 elements\n",
      "Group     2 (             NA) has   192 elements\n",
      "Group     3 (             CL) has   148 elements\n",
      "Group     4 (        Protein) has  2867 elements\n",
      "Group     5 (      Protein-H) has  1394 elements\n",
      "Group     6 (        C-alpha) has   172 elements\n",
      "Group     7 (       Backbone) has   518 elements\n",
      "Group     8 (      MainChain) has   694 elements\n",
      "Group     9 (   MainChain+Cb) has   855 elements\n",
      "Group    10 (    MainChain+H) has   863 elements\n",
      "Group    11 (      SideChain) has  2004 elements\n",
      "Group    12 (    SideChain-H) has   700 elements\n",
      "Group    13 (    Prot-Masses) has  2867 elements\n",
      "Group    14 (    non-Protein) has 166520 elements\n",
      "Group    15 (          Water) has 164277 elements\n",
      "Group    16 (            SOL) has 164277 elements\n",
      "Group    17 (      non-Water) has  5110 elements\n",
      "Group    18 (            Ion) has   340 elements\n",
      "Group    19 (             NA) has   192 elements\n",
      "Group    20 (             CL) has   148 elements\n",
      "Group    21 ( Water_and_ions) has 164617 elements\n",
      "Group    22 (!Water_and_ions) has  4770 elements\n",
      "Group    23 (           a_11) has     1 elements\n",
      "Group    24 (         a_1882) has     1 elements\n",
      "Group    25 (          a_930) has     1 elements\n",
      "Group    26 (          a_961) has     1 elements\n",
      "Group    27 (           a_11) has     1 elements\n",
      "Group    28 (         a_1882) has     1 elements\n",
      "Group    29 (          a_930) has     1 elements\n",
      "Group    30 (          a_961) has     1 elements\n",
      "Group    31 (           a_11) has     1 elements\n",
      "Group    32 (         a_1882) has     1 elements\n",
      "Group    33 (          a_930) has     1 elements\n",
      "Group    34 (          a_961) has     1 elements\n",
      "Select a group: Selected 22: '!Water_and_ions'\n",
      "Reading frame       0 time    0.000   \n",
      "Precision of GMX_run/7_prod.xtc is 0.001 (nm)\n",
      "Using output precision of 0.001 (nm)\n",
      "\n",
      "Back Off! I just backed up tmp/7_prod_1.xtc to tmp/#7_prod_1.xtc.16#\n",
      " ->  frame   1120 time 1120000.000        ->  frame   1100 time 1100000.000      \n",
      "\n",
      "\n",
      "GROMACS reminds you: \"First off, I'd suggest printing out a copy of the GNU coding standards, and NOT read it. Burn them, it's a great symbolic gesture.\" (Linus Torvalds)\n",
      "\n",
      "gmx: Relink `/opt/miniconda3/envs/moldyn/bin/../lib/././libgfortran.so.4' with `/lib/x86_64-linux-gnu/librt.so.1' for IFUNC symbol `clock_gettime'\n",
      "                     :-) GROMACS - gmx trjconv, 2018.4 (-:\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 trjconv, version 2018.4\n",
      "Executable:   /opt/miniconda3/envs/moldyn/bin/gmx\n",
      "Data prefix:  /opt/miniconda3/envs/moldyn\n",
      "Working dir:  /home/_shared/_projects/gmx_template\n",
      "Command line:\n",
      "  gmx trjconv -n GMX_system/index.ndx -f tmp/7_prod_1.xtc -s GMX_run/7_prod.tpr -o tmp/7_prod_2.xtc -pbc cluster\n",
      "\n",
      "Will write xtc: Compressed trajectory (portable xdr format): xtc\n",
      "Reading file GMX_run/7_prod.tpr, VERSION 2018.4 (single precision)\n",
      "Reading file GMX_run/7_prod.tpr, VERSION 2018.4 (single precision)\n",
      "Select group for clustering\n",
      "Group     0 (         System) has 169387 elements\n",
      "Group     1 (            DNA) has  1903 elements\n",
      "Group     2 (             NA) has   192 elements\n",
      "Group     3 (             CL) has   148 elements\n",
      "Group     4 (        Protein) has  2867 elements\n",
      "Group     5 (      Protein-H) has  1394 elements\n",
      "Group     6 (        C-alpha) has   172 elements\n",
      "Group     7 (       Backbone) has   518 elements\n",
      "Group     8 (      MainChain) has   694 elements\n",
      "Group     9 (   MainChain+Cb) has   855 elements\n",
      "Group    10 (    MainChain+H) has   863 elements\n",
      "Group    11 (      SideChain) has  2004 elements\n",
      "Group    12 (    SideChain-H) has   700 elements\n",
      "Group    13 (    Prot-Masses) has  2867 elements\n",
      "Group    14 (    non-Protein) has 166520 elements\n",
      "Group    15 (          Water) has 164277 elements\n",
      "Group    16 (            SOL) has 164277 elements\n",
      "Group    17 (      non-Water) has  5110 elements\n",
      "Group    18 (            Ion) has   340 elements\n",
      "Group    19 (             NA) has   192 elements\n",
      "Group    20 (             CL) has   148 elements\n",
      "Group    21 ( Water_and_ions) has 164617 elements\n",
      "Group    22 (!Water_and_ions) has  4770 elements\n",
      "Group    23 (           a_11) has     1 elements\n",
      "Group    24 (         a_1882) has     1 elements\n",
      "Group    25 (          a_930) has     1 elements\n",
      "Group    26 (          a_961) has     1 elements\n",
      "Group    27 (           a_11) has     1 elements\n",
      "Group    28 (         a_1882) has     1 elements\n",
      "Group    29 (          a_930) has     1 elements\n",
      "Group    30 (          a_961) has     1 elements\n",
      "Group    31 (           a_11) has     1 elements\n",
      "Group    32 (         a_1882) has     1 elements\n",
      "Group    33 (          a_930) has     1 elements\n",
      "Group    34 (          a_961) has     1 elements\n",
      "Select a group: Selected 22: '!Water_and_ions'\n",
      "Select group for output\n",
      "Group     0 (         System) has 169387 elements\n",
      "Group     1 (            DNA) has  1903 elements\n",
      "Group     2 (             NA) has   192 elements\n",
      "Group     3 (             CL) has   148 elements\n",
      "Group     4 (        Protein) has  2867 elements\n",
      "Group     5 (      Protein-H) has  1394 elements\n",
      "Group     6 (        C-alpha) has   172 elements\n",
      "Group     7 (       Backbone) has   518 elements\n",
      "Group     8 (      MainChain) has   694 elements\n",
      "Group     9 (   MainChain+Cb) has   855 elements\n",
      "Group    10 (    MainChain+H) has   863 elements\n",
      "Group    11 (      SideChain) has  2004 elements\n",
      "Group    12 (    SideChain-H) has   700 elements\n",
      "Group    13 (    Prot-Masses) has  2867 elements\n",
      "Group    14 (    non-Protein) has 166520 elements\n",
      "Group    15 (          Water) has 164277 elements\n",
      "Group    16 (            SOL) has 164277 elements\n",
      "Group    17 (      non-Water) has  5110 elements\n",
      "Group    18 (            Ion) has   340 elements\n",
      "Group    19 (             NA) has   192 elements\n",
      "Group    20 (             CL) has   148 elements\n",
      "Group    21 ( Water_and_ions) has 164617 elements\n",
      "Group    22 (!Water_and_ions) has  4770 elements\n",
      "Group    23 (           a_11) has     1 elements\n",
      "Group    24 (         a_1882) has     1 elements\n",
      "Group    25 (          a_930) has     1 elements\n",
      "Group    26 (          a_961) has     1 elements\n",
      "Group    27 (           a_11) has     1 elements\n",
      "Group    28 (         a_1882) has     1 elements\n",
      "Group    29 (          a_930) has     1 elements\n",
      "Group    30 (          a_961) has     1 elements\n",
      "Group    31 (           a_11) has     1 elements\n",
      "Group    32 (         a_1882) has     1 elements\n",
      "Group    33 (          a_930) has     1 elements\n",
      "Group    34 (          a_961) has     1 elements\n",
      "Select a group: Selected 22: '!Water_and_ions'\n",
      "Reading frame       0 time    0.000   \n",
      "Precision of tmp/7_prod_1.xtc is 0.001 (nm)\n",
      "Using output precision of 0.001 (nm)\n",
      "\n",
      "Back Off! I just backed up tmp/7_prod_2.xtc to tmp/#7_prod_2.xtc.9#\n",
      "Clustering iteration 4 of 4...\n",
      "Clustering iteration 4 of 4...0.000   \n",
      "Clustering iteration 4 of 4...0.000   \n",
      "Clustering iteration 4 of 4...0.000   \n"
     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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     ]
    },
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
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      "Clustering iteration 4 of 4...\n",
      "Clustering iteration 4 of 4...\n",
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      "Clustering iteration 4 of 4...\n",
      "Clustering iteration 4 of 4...\n",
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      "Clustering iteration 4 of 4...\n",
      "Clustering iteration 4 of 4...\n",
      "Clustering iteration 4 of 4...\n",
      "Clustering iteration 4 of 4...\n",
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      "\n",
      "\n",
      "\n",
      "GROMACS reminds you: \"The best way to obtain plausible negative examples is to run a docking program with a biophysics-based function.\" (Julie Bernauer)\n",
      "\n",
      "gmx: Relink `/opt/miniconda3/envs/moldyn/bin/../lib/././libgfortran.so.4' with `/lib/x86_64-linux-gnu/librt.so.1' for IFUNC symbol `clock_gettime'\n",
      "                     :-) GROMACS - gmx trjconv, 2018.4 (-:\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 trjconv, version 2018.4\n",
      "Executable:   /opt/miniconda3/envs/moldyn/bin/gmx\n",
      "Data prefix:  /opt/miniconda3/envs/moldyn\n",
      "Working dir:  /home/_shared/_projects/gmx_template\n",
      "Command line:\n",
      "  gmx trjconv -f tmp/7_prod_2.xtc -s GMX_system/sys_ref.pdb -o big_data/sys_md.xtc -fit rot+trans\n",
      "\n",
      "Will write xtc: Compressed trajectory (portable xdr format): xtc\n",
      "\n",
      "WARNING: Masses and atomic (Van der Waals) radii will be guessed\n",
      "         based on residue and atom names, since they could not be\n",
      "         definitively assigned from the information in your input\n",
      "         files. These guessed numbers might deviate from the mass\n",
      "         and radius of the atom type. Please check the output\n",
      "         files if necessary.\n",
      "\n",
      "\n",
      "WARNING: If there are molecules in the input trajectory file\n",
      "         that are broken across periodic boundaries, they\n",
      "         cannot be made whole (or treated as whole) without\n",
      "         you providing a run input file.\n",
      "\n",
      "Select group for least squares fit\n",
      "Group     0 (         System) has  4770 elements\n",
      "Group     1 (            DNA) has  1903 elements\n",
      "Group     2 (        Protein) has  2867 elements\n",
      "Group     3 (      Protein-H) has  1394 elements\n",
      "Group     4 (        C-alpha) has   172 elements\n",
      "Group     5 (       Backbone) has   518 elements\n",
      "Group     6 (      MainChain) has   694 elements\n",
      "Group     7 (   MainChain+Cb) has   855 elements\n",
      "Group     8 (    MainChain+H) has   863 elements\n",
      "Group     9 (      SideChain) has  2004 elements\n",
      "Group    10 (    SideChain-H) has   700 elements\n",
      "Group    11 (    Prot-Masses) has  2867 elements\n",
      "Group    12 (    non-Protein) has  1903 elements\n",
      "Select a group: Selected 0: 'System'\n",
      "Select group for output\n",
      "Group     0 (         System) has  4770 elements\n",
      "Group     1 (            DNA) has  1903 elements\n",
      "Group     2 (        Protein) has  2867 elements\n",
      "Group     3 (      Protein-H) has  1394 elements\n",
      "Group     4 (        C-alpha) has   172 elements\n",
      "Group     5 (       Backbone) has   518 elements\n",
      "Group     6 (      MainChain) has   694 elements\n",
      "Group     7 (   MainChain+Cb) has   855 elements\n",
      "Group     8 (    MainChain+H) has   863 elements\n",
      "Group     9 (      SideChain) has  2004 elements\n",
      "Group    10 (    SideChain-H) has   700 elements\n",
      "Group    11 (    Prot-Masses) has  2867 elements\n",
      "Group    12 (    non-Protein) has  1903 elements\n",
      "Select a group: Selected 0: 'System'\n",
      "Reading frame       0 time    0.000   \n",
      "Precision of tmp/7_prod_2.xtc is 0.001 (nm)\n",
      "Using output precision of 0.001 (nm)\n",
      "\n",
      "Back Off! I just backed up big_data/sys_md.xtc to big_data/#sys_md.xtc.5#\n",
      " ->  frame   1120 time 1120000.000        ->  frame   1100 time 1100000.000      \n",
      "\n",
      "\n",
      "GROMACS reminds you: \"I have not failed. I've just found 10,000 ways that won't work\" (Thomas Alva Edison)\n",
      "\n"
     ]
    }
   ],
   "source": [
    "#The code below was collapsed to one shell file\n",
    "!./5_trj_preprocessing.sh 7_prod sys_md"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Old version below is inactive"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "%%bash\n",
    "mkdir -p tmp\n",
    "mkdir -p big_data\n",
    "#The group here may need to be adjusted if you have other components except protein, e.g. DNA\n",
    "gmx trjconv -n GMX_system/index.ndx -f GMX_run/7_prod.xtc -s GMX_run/7_prod.tpr -o tmp/7_prod_1.xtc -pbc whole << !\n",
    "!Water_and_ions\n",
    "!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "%%bash --out out\n",
    "gmx trjconv -n GMX_system/index.ndx -f tmp/7_prod_1.xtc -s GMX_run/7_prod.tpr -o tmp/7_prod_2.xtc -pbc cluster << !\n",
    "!Water_and_ions\n",
    "!Water_and_ions\n",
    "!"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "%%bash\n",
    "gmx trjconv  -f tmp/7_prod_2.xtc -s GMX_system/sys_ref.pdb -o big_data/sys_md.xtc -fit rot+trans << !\n",
    "System\n",
    "System\n",
    "!"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": []
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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