Multiply out a single PDB file using MDAnalysis (similar to editconf in Gromacs)

PDB_multiple.ipynb

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   "cell_type": "code",
   "execution_count": 1,
   "metadata": {
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   "outputs": [],
   "source": [
    "import MDAnalysis as mda\n",
    "import numpy as np"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {
    "collapsed": true
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   "outputs": [],
   "source": [
    "def box_iter(size):\n",
    "    Nx, Ny, Nz = size\n",
    "    for x in range(Nx):\n",
    "        for y in range(Ny):\n",
    "            for z in range(Nz):\n",
    "                yield x, y, z"
   ]
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     "text": [
      "/home/richard/miniconda2/envs/mdadev/lib/python2.7/site-packages/MDAnalysis/topology/guessers.py:56: UserWarning: Failed to guess the mass for the following atom types: Z\n",
      "  \"\".format(', '.join(misses)))\n"
     ]
    }
   ],
   "source": [
    "u = mda.Universe('single.pdb')\n",
    "# set dimensions to what I know a single unit cell to be\n",
    "u.dimensions = [51.664 / 2.0] * 3 + [90] * 3"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {
    "collapsed": false
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   "outputs": [
    {
     "data": {
      "text/plain": [
       "<AtomGroup with 424 atoms>"
      ]
     },
     "execution_count": 4,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u.atoms"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ 25.83200073,  25.83200073,  25.83200073,  90.        ,\n",
       "        90.        ,  90.        ], dtype=float32)"
      ]
     },
     "execution_count": 5,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u.dimensions"
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  {
   "cell_type": "code",
   "execution_count": 9,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "def make_universe(size):\n",
    "    box = np.array([51.664 / 2.0] * 3)\n",
    "    \n",
    "    unis = []\n",
    "    for x, y, z in box_iter(size):\n",
    "        u = mda.Universe('single.pdb')\n",
    "        u.atoms.translate(box * (x, y, z))\n",
    "        \n",
    "        unis.append(u.atoms)\n",
    "    \n",
    "    new_u = mda.Merge(*unis)\n",
    "    new_u.dimensions = list(box * size) + [90.] * 3\n",
    "    \n",
    "    return new_u"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 10,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "u = make_universe((2, 2, 2))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 11,
   "metadata": {
    "collapsed": false
   },
   "outputs": [
    {
     "data": {
      "text/plain": [
       "array([ 51.66400146,  51.66400146,  51.66400146,  90.        ,\n",
       "        90.        ,  90.        ], dtype=float32)"
      ]
     },
     "execution_count": 11,
     "metadata": {},
     "output_type": "execute_result"
    }
   ],
   "source": [
    "u.dimensions"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 47,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "u.atoms.write('larger.pdb')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": []
  }
 ],
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Why have the merged universe vectors doubled instead of tripled? Along the x axis for example are you not tiling before and after the primary cell to have L (before) + L (primary unit cell) + L (after) total length--around 75 instead of 51?