{
 "cells": [
  {
   "cell_type": "markdown",
   "id": "7a703c5f",
   "metadata": {},
   "source": [
    "# Notebook03: POPC/POPE mixture\n",
    "\n",
    "In this notebook, we will show you how to reconstruct hydrogens, calculate the order parameters and produce output trajectories on a POPC/POPE (50:50) mixture. Again, this example is based on the Berger united-atom force field.\n",
    "\n",
    "Before going on, we advise you to get started with [Notebook01](Notebook_01_buildH_calc_OP.ipynb) if you are not familiar with basic features of **buildH** and Jupyter notebooks (e.g. do you know what `!` means in a Jupyter cell?). \n",
    "\n",
    "## Checking buildH activation\n",
    "\n",
    "As explained in [Notebook01](Notebook_01_buildH_calc_OP.ipynb), you should have activated **buildH** before launching this notebook, thus you should obtain the following when invoking `buildH` in a Unix terminal:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "id": "9fe5a816",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "usage: buildH [-h] [-v] -c COORD [-t TRAJ] -l LIPID\n",
      "              [-lt LIPID_TOPOLOGY [LIPID_TOPOLOGY ...]] -d DEFOP\n",
      "              [-opx OPDBXTC] [-o OUT] [-b BEGIN] [-e END] [-igch3]\n",
      "buildH: error: the following arguments are required: -c/--coord, -l/--lipid, -d/--defop\n",
      "\u001b[0m"
     ]
    }
   ],
   "source": [
    "!buildH"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "808ca76e",
   "metadata": {},
   "source": [
    "If you see this, you can go on. If not, please go to `Notebook01` and see the explanations there on how to activate **buildH**.\n",
    "\n",
    "## Downloading the example files\n",
    "\n",
    "The example shown in this Notebook are taken from a POPC/POPE (50:50) trajectory of 256 lipids taken from the [NMRlipidsIVb project](http://nmrlipids.blogspot.com/2021/03/nmrlipids-ivb-toward-submission-of.html). The initial source files can be found on [Zenodo](https://zenodo.org/record/1402449). For the purpose of learning, we simplified the trajectory and extracted only 25 frames (0-25 ns, one frame / ns). The starting gro file and the trajectory of 25 frames can be directly downloaded from the **buildH** repo in the directory https://github.com/patrickfuchs/buildH/tree/master/docs/Berger_POPCPOPE_test_case. Here we'll download them with `wget` (recall to download all files in raw format):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "id": "0dd9c85a",
   "metadata": {
    "scrolled": true
   },
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2021-07-07 15:12:13--  https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCPOPE_test_case/start.gro\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.108.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 2097099 (2.0M) [text/plain]\n",
      "Saving to: ‘start.gro’\n",
      "\n",
      "start.gro           100%[===================>]   2.00M  --.-KB/s    in 0.06s   \n",
      "\n",
      "2021-07-07 15:12:13 (32.2 MB/s) - ‘start.gro’ saved [2097099/2097099]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCPOPE_test_case/start.gro"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "id": "28b93568",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2021-07-07 15:12:28--  https://github.com/patrickfuchs/buildH/raw/master/docs/Berger_POPCPOPE_test_case/md_0_25ns_dt1000.xtc\n",
      "Resolving github.com (github.com)... 140.82.121.4\n",
      "Connecting to github.com (github.com)|140.82.121.4|:443... connected.\n",
      "HTTP request sent, awaiting response... 302 Found\n",
      "Location: https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCPOPE_test_case/md_0_25ns_dt1000.xtc [following]\n",
      "--2021-07-07 15:12:29--  https://raw.githubusercontent.com/patrickfuchs/buildH/master/docs/Berger_POPCPOPE_test_case/md_0_25ns_dt1000.xtc\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.109.133, 185.199.110.133, 185.199.111.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.109.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 4458540 (4.3M) [application/octet-stream]\n",
      "Saving to: ‘md_0_25ns_dt1000.xtc’\n",
      "\n",
      "md_0_25ns_dt1000.xt 100%[===================>]   4.25M  --.-KB/s    in 0.08s   \n",
      "\n",
      "2021-07-07 15:12:29 (56.1 MB/s) - ‘md_0_25ns_dt1000.xtc’ saved [4458540/4458540]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://github.com/patrickfuchs/buildH/raw/master/docs/Berger_POPCPOPE_test_case/md_0_25ns_dt1000.xtc"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "id": "87e085c4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "data\n",
      "img\n",
      "md_0_25ns_dt1000.xtc\n",
      "Notebook_01_buildH_calc_OP.ipynb\n",
      "Notebook_02_buildH_calc_OP_outputwH.ipynb\n",
      "Notebook_03_mixture_POPC_POPE.ipynb\n",
      "Notebook_04_library.ipynb\n",
      "Notebook_05_mixture_POPC_cholesterol.ipynb\n",
      "start.gro\n"
     ]
    }
   ],
   "source": [
    "!ls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "e3919d24",
   "metadata": {},
   "source": [
    "We also need the two def files corresponding to POPC and POPE. They can be downloaded from the **buildH** repo in the directory https://github.com/patrickfuchs/buildH/tree/master/def_files (again remember to use raw files):"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "id": "d4f09307",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2021-07-07 15:12:52--  https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPC.def\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.111.133, 185.199.108.133, 185.199.109.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.111.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 2135 (2.1K) [text/plain]\n",
      "Saving to: ‘Berger_POPC.def’\n",
      "\n",
      "Berger_POPC.def     100%[===================>]   2.08K  --.-KB/s    in 0.001s  \n",
      "\n",
      "2021-07-07 15:12:53 (2.00 MB/s) - ‘Berger_POPC.def’ saved [2135/2135]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPC.def"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 6,
   "id": "f8fe0ee4",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "--2021-07-07 15:12:56--  https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPE.def\n",
      "Resolving raw.githubusercontent.com (raw.githubusercontent.com)... 185.199.110.133, 185.199.111.133, 185.199.108.133, ...\n",
      "Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443... connected.\n",
      "HTTP request sent, awaiting response... 200 OK\n",
      "Length: 1937 (1.9K) [text/plain]\n",
      "Saving to: ‘Berger_POPE.def’\n",
      "\n",
      "Berger_POPE.def     100%[===================>]   1.89K  --.-KB/s    in 0.001s  \n",
      "\n",
      "2021-07-07 15:12:56 (1.98 MB/s) - ‘Berger_POPE.def’ saved [1937/1937]\n",
      "\n"
     ]
    }
   ],
   "source": [
    "!wget https://raw.githubusercontent.com/patrickfuchs/buildH/master/def_files/Berger_POPE.def"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 7,
   "id": "cb8a936b",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Berger_POPC.def\t\t\t  Notebook_02_buildH_calc_OP_outputwH.ipynb\n",
      "Berger_POPE.def\t\t\t  Notebook_03_mixture_POPC_POPE.ipynb\n",
      "data\t\t\t\t  Notebook_04_library.ipynb\n",
      "img\t\t\t\t  Notebook_05_mixture_POPC_cholesterol.ipynb\n",
      "md_0_25ns_dt1000.xtc\t\t  start.gro\n",
      "Notebook_01_buildH_calc_OP.ipynb\n"
     ]
    }
   ],
   "source": [
    "!ls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "91b6ec3d",
   "metadata": {},
   "source": [
    "Recall, the def files present on the **buildH** `def_files` directory contain all the possible (apolar) H that can be reconstructed on each lipids. The polar hydrogens are already present (e.g. the different N-H of the ethanolamine in POPE), thus they do not need to be reconstructed. **buildH** will let them as is, like all other non apolar H atoms.\n",
    "\n",
    "## Dealing with POPC\n",
    "\n",
    "When we have a mixture of lipids, **buildH** cannot reconstruct hydrogens on all lipids at the same time. So we start with H reconstruction and OP calculation on POPC (we'll focus on POPE later). Since Berger POPC is a supported lipid, we can launch easily **buildH** with the classical flags: `-c` for reading the initial pdb or gro file, `-t` for reading the trajectory, `-l` for specifying the type of lipid, `-d` for specifying the def file, `-o` for the output file with order parameters, and last `-opx` for the output trajectory with hydrogens (recall not to put any extension, they'll be added automatically by **buildH**). Importantly, when we want to output a trajectory with newly reconstructed hydrogens (option `-opx`), *all possible H to reconstruct need to be present in the def file*. This is fine since this is the case for all lipids in the [def file directory](https://github.com/patrickfuchs/buildH/tree/master/def_files) of the  **buildH** repository."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 8,
   "id": "79174caf",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Constructing the system...\n",
      "System has 46600 atoms\n",
      "Writing new pdb with hydrogens.\n",
      "Writing trajectory with hydrogens in xtc file.\n",
      "Dealing with frame 0 at 0.0 ps.\n",
      "Dealing with frame 1 at 1000.0 ps.\n",
      "Dealing with frame 2 at 2000.0 ps.\n",
      "Dealing with frame 3 at 3000.0 ps.\n",
      "Dealing with frame 4 at 4000.0 ps.\n",
      "Dealing with frame 5 at 5000.0 ps.\n",
      "Dealing with frame 6 at 6000.0 ps.\n",
      "Dealing with frame 7 at 7000.0 ps.\n",
      "Dealing with frame 8 at 8000.0 ps.\n",
      "Dealing with frame 9 at 9000.0 ps.\n",
      "Dealing with frame 10 at 10000.0 ps.\n",
      "Dealing with frame 11 at 11000.0 ps.\n",
      "Dealing with frame 12 at 12000.0 ps.\n",
      "Dealing with frame 13 at 13000.0 ps.\n",
      "Dealing with frame 14 at 14000.0 ps.\n",
      "Dealing with frame 15 at 15000.0 ps.\n",
      "Dealing with frame 16 at 16000.0 ps.\n",
      "Dealing with frame 17 at 17000.0 ps.\n",
      "Dealing with frame 18 at 18000.0 ps.\n",
      "Dealing with frame 19 at 19000.0 ps.\n",
      "Dealing with frame 20 at 20000.0 ps.\n",
      "Dealing with frame 21 at 21000.0 ps.\n",
      "Dealing with frame 22 at 22000.0 ps.\n",
      "Dealing with frame 23 at 23000.0 ps.\n",
      "Dealing with frame 24 at 24000.0 ps.\n",
      "Dealing with frame 25 at 25000.0 ps.\n",
      "Results written to OP_POPC.dat\n",
      "\u001b[0m"
     ]
    }
   ],
   "source": [
    "!buildH -c start.gro -l Berger_POPC -t md_0_25ns_dt1000.xtc -d Berger_POPC.def -o OP_POPC.dat -opx traj_POPC_wH"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 9,
   "id": "c459ebcd",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Berger_POPC.def\n",
      "Berger_POPE.def\n",
      "data\n",
      "img\n",
      "md_0_25ns_dt1000.xtc\n",
      "Notebook_01_buildH_calc_OP.ipynb\n",
      "Notebook_02_buildH_calc_OP_outputwH.ipynb\n",
      "Notebook_03_mixture_POPC_POPE.ipynb\n",
      "Notebook_04_library.ipynb\n",
      "Notebook_05_mixture_POPC_cholesterol.ipynb\n",
      "OP_POPC.dat\n",
      "start.gro\n",
      "traj_POPC_wH.pdb\n",
      "traj_POPC_wH.xtc\n"
     ]
    }
   ],
   "source": [
    "!ls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "f11f0273",
   "metadata": {},
   "source": [
    "The order parameters of POPC lipids have been written to the file `OP_POPC.dat`"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "id": "69396299",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# OP_name            resname atom1 atom2  OP_mean OP_stddev OP_stem\n",
      "#--------------------------------------------------------------------\n",
      "gamma1_1             POPC    C1    H11   -0.00343  0.12015  0.01062\n",
      "gamma1_2             POPC    C1    H12    0.00752  0.09808  0.00867\n",
      "gamma1_3             POPC    C1    H13   -0.00614  0.08702  0.00769\n",
      "gamma2_1             POPC    C2    H21   -0.00397  0.11983  0.01059\n",
      "gamma2_2             POPC    C2    H22   -0.00703  0.09226  0.00816\n",
      "gamma2_3             POPC    C2    H23   -0.00952  0.10068  0.00890\n",
      "gamma3_1             POPC    C3    H31    0.00060  0.12174  0.01076\n",
      "gamma3_2             POPC    C3    H32   -0.00474  0.09119  0.00806\n"
     ]
    }
   ],
   "source": [
    "!head OP_POPC.dat"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "d9194ef3",
   "metadata": {},
   "source": [
    "A pdb `traj_POPC_wH.pdb` and an xtc `traj_POPC_wH.xtc` file have been produced with hydrogens on POPC only. So let's check whether the POPC have hydrogens and not POPE:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "id": "f70f9cc9",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ATOM      1  C1  POPC    1      89.160   7.570  22.770  1.00  0.00             C\n",
      "ATOM      2  H11 POPC    1      88.713   8.530  23.029  1.00  0.00             H\n",
      "ATOM      3  H12 POPC    1      88.372   6.843  22.577  1.00  0.00             H\n",
      "ATOM      4  H13 POPC    1      89.775   7.684  21.878  1.00  0.00             H\n",
      "ATOM      5  C2  POPC    1      89.200   7.090  25.120  1.00  0.00             C\n",
      "ATOM      6  H21 POPC    1      88.733   8.065  25.257  1.00  0.00             H\n",
      "ATOM      7  H22 POPC    1      89.845   6.873  25.971  1.00  0.00             H\n",
      "ATOM      8  H23 POPC    1      88.428   6.324  25.045  1.00  0.00             H\n",
      "ATOM      9  C3  POPC    1      91.030   8.130  24.080  1.00  0.00             C\n",
      "ATOM     10  H31 POPC    1      90.552   9.093  24.258  1.00  0.00             H\n",
      "ATOM     11  H32 POPC    1      91.651   8.192  23.186  1.00  0.00             H\n",
      "ATOM     12  H33 POPC    1      91.651   7.869  24.937  1.00  0.00             H\n",
      "ATOM     13  N4  POPC    1      90.000   7.100  23.890  1.00  0.00             N\n",
      "ATOM     14  C5  POPC    1      90.660   5.800  23.650  1.00  0.00             C\n",
      "ATOM     15  H51 POPC    1      91.220   5.539  24.548  1.00  0.00             H\n",
      "ATOM     16  H52 POPC    1      91.350   5.924  22.815  1.00  0.00             H\n",
      "ATOM     17  C6  POPC    1      89.730   4.630  23.320  1.00  0.00             C\n",
      "ATOM     18  H61 POPC    1      89.359   4.775  22.305  1.00  0.00             H\n",
      "ATOM     19  H62 POPC    1      88.895   4.660  24.020  1.00  0.00             H\n",
      "ATOM     20  O7  POPC    1      90.310   3.330  23.390  1.00  0.00             O\n",
      "grep: write error: Broken pipe\n"
     ]
    }
   ],
   "source": [
    "!grep POPC traj_POPC_wH.pdb | head -20"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 12,
   "id": "049bbfae",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ATOM  17153  H1  POPE  129      82.600  -2.110  24.640  1.00  0.00             H\n",
      "ATOM  17154  H2  POPE  129      82.290  -1.570  23.100  1.00  0.00             H\n",
      "ATOM  17155  H3  POPE  129      83.140  -0.610  24.130  1.00  0.00             H\n",
      "ATOM  17156  N4  POPE  129      82.400  -1.300  24.070  1.00  0.00             N\n",
      "ATOM  17157  C5  POPE  129      81.140  -0.680  24.510  1.00  0.00             C\n",
      "ATOM  17158  C6  POPE  129      80.830   0.480  23.550  1.00  0.00             C\n",
      "ATOM  17159  O7  POPE  129      81.880   1.450  23.530  1.00  0.00             O\n",
      "ATOM  17160  P8  POPE  129      81.420   2.670  22.580  1.00  0.00             P\n",
      "ATOM  17161  O9  POPE  129      82.620   3.440  22.200  1.00  0.00             O\n",
      "ATOM  17162  O10 POPE  129      80.420   2.190  21.610  1.00  0.00             O\n",
      "ATOM  17163  O11 POPE  129      80.600   3.490  23.700  1.00  0.00             O\n",
      "ATOM  17164  C12 POPE  129      81.550   4.230  24.480  1.00  0.00             C\n",
      "ATOM  17165  C13 POPE  129      80.830   5.150  25.470  1.00  0.00             C\n",
      "ATOM  17166  O14 POPE  129      81.780   5.780  26.340  1.00  0.00             O\n",
      "ATOM  17167  C15 POPE  129      82.000   7.120  26.230  1.00  0.00             C\n",
      "ATOM  17168  O16 POPE  129      81.490   7.750  25.300  1.00  0.00             O\n",
      "ATOM  17169  C17 POPE  129      83.030   7.710  27.190  1.00  0.00             C\n",
      "ATOM  17170  C18 POPE  129      82.420   8.040  28.550  1.00  0.00             C\n",
      "ATOM  17171  C19 POPE  129      81.550   9.300  28.470  1.00  0.00             C\n",
      "ATOM  17172  C20 POPE  129      80.810   9.530  29.790  1.00  0.00             C\n",
      "grep: write error: Broken pipe\n"
     ]
    }
   ],
   "source": [
    "!grep POPE traj_POPC_wH.pdb | head -20"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "046dfef0",
   "metadata": {},
   "source": [
    "Yeah that is fine! POPC have all hydrogens reconstructed, while POPE do not (we can only see the polar hydrogens which are natively present in a united-atom structure)."
   ]
  },
  {
   "cell_type": "markdown",
   "id": "b52fadb7",
   "metadata": {},
   "source": [
    "## Dealing with POPE\n",
    "\n",
    "Now that POPC have all hydrogens, we can restart from that pdb file to reconstruct the hydrogens of POPE. Thus we can use the flags `-c` with the pdb file we just generated `traj_POPC_wH.pdb` (Hs on POPC but not POPE). The `-t` will be used with the same trajectory with H on POPC (but not POPE!) `traj_POPC_wH.xtc`. We output order parameters for POPE with `-o`. Last, `-opx` will produce a file with hydrogens on POPE."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 13,
   "id": "713f658d",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Constructing the system...\n",
      "System has 57096 atoms\n",
      "Writing new pdb with hydrogens.\n",
      "Writing trajectory with hydrogens in xtc file.\n",
      "Dealing with frame 0 at 0.0 ps.\n",
      "Dealing with frame 1 at 0.0 ps.\n",
      "Dealing with frame 2 at 0.0 ps.\n",
      "Dealing with frame 3 at 0.0 ps.\n",
      "Dealing with frame 4 at 0.0 ps.\n",
      "Dealing with frame 5 at 0.0 ps.\n",
      "Dealing with frame 6 at 0.0 ps.\n",
      "Dealing with frame 7 at 0.0 ps.\n",
      "Dealing with frame 8 at 0.0 ps.\n",
      "Dealing with frame 9 at 0.0 ps.\n",
      "Dealing with frame 10 at 0.0 ps.\n",
      "Dealing with frame 11 at 0.0 ps.\n",
      "Dealing with frame 12 at 0.0 ps.\n",
      "Dealing with frame 13 at 0.0 ps.\n",
      "Dealing with frame 14 at 0.0 ps.\n",
      "Dealing with frame 15 at 0.0 ps.\n",
      "Dealing with frame 16 at 0.0 ps.\n",
      "Dealing with frame 17 at 0.0 ps.\n",
      "Dealing with frame 18 at 0.0 ps.\n",
      "Dealing with frame 19 at 0.0 ps.\n",
      "Dealing with frame 20 at 0.0 ps.\n",
      "Dealing with frame 21 at 0.0 ps.\n",
      "Dealing with frame 22 at 0.0 ps.\n",
      "Dealing with frame 23 at 0.0 ps.\n",
      "Dealing with frame 24 at 0.0 ps.\n",
      "Dealing with frame 25 at 0.0 ps.\n",
      "Results written to OP_POPE.dat\n",
      "\u001b[0m"
     ]
    }
   ],
   "source": [
    "!buildH -c traj_POPC_wH.pdb -l Berger_POPE -t traj_POPC_wH.xtc -d Berger_POPE.def -o OP_POPE.dat -opx traj_POPCPOPE_wH"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 14,
   "id": "c4f03dc7",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "Berger_POPC.def\n",
      "Berger_POPE.def\n",
      "data\n",
      "img\n",
      "md_0_25ns_dt1000.xtc\n",
      "Notebook_01_buildH_calc_OP.ipynb\n",
      "Notebook_02_buildH_calc_OP_outputwH.ipynb\n",
      "Notebook_03_mixture_POPC_POPE.ipynb\n",
      "Notebook_04_library.ipynb\n",
      "Notebook_05_mixture_POPC_cholesterol.ipynb\n",
      "OP_POPC.dat\n",
      "OP_POPE.dat\n",
      "start.gro\n",
      "traj_POPCPOPE_wH.pdb\n",
      "traj_POPCPOPE_wH.xtc\n",
      "traj_POPC_wH.pdb\n",
      "traj_POPC_wH.xtc\n"
     ]
    }
   ],
   "source": [
    "!ls"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "0c606845",
   "metadata": {},
   "source": [
    "Great, we can now look at the order parameters of POPE:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 15,
   "id": "837ea0fb",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "# OP_name            resname atom1 atom2  OP_mean OP_stddev OP_stem\n",
      "#--------------------------------------------------------------------\n",
      "beta1                POPE    C5    H51    0.18091  0.44608  0.03943\n",
      "beta2                POPE    C5    H52   -0.04410  0.44630  0.03945\n",
      "alpha1               POPE    C6    H61    0.08958  0.45722  0.04041\n",
      "alpha2               POPE    C6    H62    0.19382  0.46467  0.04107\n",
      "g3_1                 POPE    C12   H121  -0.27276  0.26619  0.02353\n",
      "g3_2                 POPE    C12   H122  -0.18926  0.29892  0.02642\n",
      "g2_1                 POPE    C13   H131  -0.15531  0.32935  0.02911\n",
      "g1_1                 POPE    C32   H321   0.12967  0.45277  0.04002\n"
     ]
    }
   ],
   "source": [
    "!head OP_POPE.dat"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "6b7d076c",
   "metadata": {},
   "source": [
    "And check whether POPC **and** POPE have all hydrogens reconstructed:"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 16,
   "id": "73fc7da5",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ATOM  17153  H1  POPE  129      82.600  -2.110  24.640  1.00  0.00             H\n",
      "ATOM  17154  H2  POPE  129      82.290  -1.570  23.100  1.00  0.00             H\n",
      "ATOM  17155  H3  POPE  129      83.140  -0.610  24.130  1.00  0.00             H\n",
      "ATOM  17156  N4  POPE  129      82.400  -1.300  24.070  1.00  0.00             N\n",
      "ATOM  17157  C5  POPE  129      81.140  -0.680  24.510  1.00  0.00             C\n",
      "ATOM  17158  H51 POPE  129      81.247  -0.302  25.527  1.00  0.00             H\n",
      "ATOM  17159  H52 POPE  129      80.334  -1.414  24.478  1.00  0.00             H\n",
      "ATOM  17160  C6  POPE  129      80.830   0.480  23.550  1.00  0.00             C\n",
      "ATOM  17161  H61 POPE  129      79.908   0.965  23.870  1.00  0.00             H\n",
      "ATOM  17162  H62 POPE  129      80.700   0.080  22.544  1.00  0.00             H\n",
      "ATOM  17163  O7  POPE  129      81.880   1.450  23.530  1.00  0.00             O\n",
      "ATOM  17164  P8  POPE  129      81.420   2.670  22.580  1.00  0.00             P\n",
      "ATOM  17165  O9  POPE  129      82.620   3.440  22.200  1.00  0.00             O\n",
      "ATOM  17166  O10 POPE  129      80.420   2.190  21.610  1.00  0.00             O\n",
      "ATOM  17167  O11 POPE  129      80.600   3.490  23.700  1.00  0.00             O\n",
      "ATOM  17168  C12 POPE  129      81.550   4.230  24.480  1.00  0.00             C\n",
      "ATOM  17169 H121 POPE  129      82.169   4.833  23.815  1.00  0.00             H\n",
      "ATOM  17170 H122 POPE  129      82.181   3.534  25.032  1.00  0.00             H\n",
      "ATOM  17171  C13 POPE  129      80.830   5.150  25.470  1.00  0.00             C\n",
      "ATOM  17172 H131 POPE  129      80.311   5.977  24.987  1.00  0.00             H\n",
      "grep: write error: Broken pipe\n"
     ]
    }
   ],
   "source": [
    "!grep POPE traj_POPCPOPE_wH.pdb | head -20"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 17,
   "id": "d0ac2551",
   "metadata": {},
   "outputs": [
    {
     "name": "stdout",
     "output_type": "stream",
     "text": [
      "ATOM      1  C1  POPC    1      89.160   7.570  22.770  1.00  0.00             C\n",
      "ATOM      2  H11 POPC    1      88.710   8.530  23.030  1.00  0.00             H\n",
      "ATOM      3  H12 POPC    1      88.370   6.840  22.580  1.00  0.00             H\n",
      "ATOM      4  H13 POPC    1      89.780   7.680  21.880  1.00  0.00             H\n",
      "ATOM      5  C2  POPC    1      89.200   7.090  25.120  1.00  0.00             C\n",
      "ATOM      6  H21 POPC    1      88.730   8.060  25.260  1.00  0.00             H\n",
      "ATOM      7  H22 POPC    1      89.850   6.870  25.970  1.00  0.00             H\n",
      "ATOM      8  H23 POPC    1      88.430   6.320  25.050  1.00  0.00             H\n",
      "ATOM      9  C3  POPC    1      91.030   8.130  24.080  1.00  0.00             C\n",
      "ATOM     10  H31 POPC    1      90.550   9.090  24.260  1.00  0.00             H\n",
      "ATOM     11  H32 POPC    1      91.650   8.190  23.190  1.00  0.00             H\n",
      "ATOM     12  H33 POPC    1      91.650   7.870  24.940  1.00  0.00             H\n",
      "ATOM     13  N4  POPC    1      90.000   7.100  23.890  1.00  0.00             N\n",
      "ATOM     14  C5  POPC    1      90.660   5.800  23.650  1.00  0.00             C\n",
      "ATOM     15  H51 POPC    1      91.220   5.540  24.550  1.00  0.00             H\n",
      "ATOM     16  H52 POPC    1      91.350   5.920  22.820  1.00  0.00             H\n",
      "ATOM     17  C6  POPC    1      89.730   4.630  23.320  1.00  0.00             C\n",
      "ATOM     18  H61 POPC    1      89.360   4.780  22.310  1.00  0.00             H\n",
      "ATOM     19  H62 POPC    1      88.900   4.660  24.020  1.00  0.00             H\n",
      "ATOM     20  O7  POPC    1      90.310   3.330  23.390  1.00  0.00             O\n",
      "grep: write error: Broken pipe\n"
     ]
    }
   ],
   "source": [
    "!grep POPC traj_POPCPOPE_wH.pdb | head -20"
   ]
  },
  {
   "cell_type": "markdown",
   "id": "16a5a4c4",
   "metadata": {},
   "source": [
    "## Conclusion\n",
    "\n",
    "In this notebook, we showed you how to use **buildH** on a mixture of POPC/POPE lipids. **buildH** has to be launched for each lipid separately. If a trajectory with all hydrogens on all lipids is wanted, one has to produce intermediate trajectories at each step. In the figure below is shown the two step process (image rendered with [VMD](https://www.ks.uiuc.edu/Research/vmd/)).\n",
    "\n",
    "![H reconstruction on a POPC/POPE mixture with buildH](img/addH_POPC_POPE.png)"
   ]
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "Python 3 (ipykernel)",
   "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": "3.8.10"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 5
}