{
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  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "slideshow": {
     "slide_type": "skip"
    }
   },
   "outputs": [],
   "source": [
    "from htmd.ui import *"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "# Molecular dynamics protocols in HTMD"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "-"
    }
   },
   "source": [
    "Summary: How to equilibrate and prepare a system for productive simulations"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Build a sample system"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false,
    "slideshow": {
     "slide_type": "-"
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   "outputs": [],
   "source": [
    "tryp = Molecule(\"3PTB\")\n",
    "tryp.remove(\"resname BEN\")\n",
    "tryp_op = proteinPrepare(tryp)\n",
    "tryp_seg = autoSegment(tryp_op)\n",
    "tryp_solv = solvate(tryp_seg,pad=10)\n",
    "#tryp_amber = amber.build(tryp_solv, param= [\"frcmod.ionslrcm_cm_tip3p\"], outdir='build-amber')\n",
    "tryp_charmm = charmm.build(tryp_solv, outdir='build-charmm')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Equilibration protocol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "from htmd.protocols.equilibration_v2 import Equilibration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "md = Equilibration()\n",
    "md.runtime = 1000\n",
    "md.timeunits = 'fs'\n",
    "md.temperature = 300\n",
    "md.useconstantratio = False  # only for membrane sims\n",
    "# this is only needed for setting the flatbottom potential, otherwise remove it\n",
    "# md.fb_reference = 'protein and resid 293'\n",
    "# md.fb_selection = 'segname L and noh'\n",
    "# md.fb_box = [-25, 25, -25, 25, 43, 45]\n",
    "# md.fb_k = 5\n",
    "md.write('./build-charmm/','./equil')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "%ls equil/"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Run the equilibration"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "local = LocalGPUQueue()\n",
    "local.submit('./equil/')\n",
    "local.wait()"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {
    "collapsed": false,
    "slideshow": {
     "slide_type": "slide"
    }
   },
   "source": [
    "## Production protocol"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "from htmd.protocols.production_v4 import Production"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": true
   },
   "outputs": [],
   "source": [
    "md = Production()\n",
    "md.runtime = 10\n",
    "md.timeunits = 'ns'\n",
    "md.temperature  = 300\n",
    "md.acemd.bincoordinates = 'output.coor'\n",
    "md.acemd.extendedsystem  = 'output.xsc'\n",
    "md.write('equil','prod')"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Run the production"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {
    "collapsed": false
   },
   "outputs": [],
   "source": [
    "local = LocalGPUQueue()\n",
    "local.submit('./prod/')\n",
    "local.wait()"
   ]
  }
 ],
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