{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# 10. Writing mapped trajectories from Gromacs all atom (AA) trajectories\n", "\n", "### Prerequisites\n", "* MDAnalysis\n", "* gsd\n", "\n", "This example maps a system of two 12 amino acid long peptides. One amino acid residue's center of mass represents one CG bead. The all atom topology and trajectory files can be found in `examples` directory. The mapped trajectory will be saved in gsd format to `CG_tutorial` directory. " ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "import hoomd\n", "import numpy as np \n", "import hoomd.md\n", "import gsd,gsd.hoomd\n", "import gsd.pygsd\n", "import hoomd.htf as htf\n", "import tensorflow as tf\n", "import MDAnalysis as mda\n", "\n", "# disable GPU\n", "import os\n", "os.environ['CUDA_VISIBLE_DEVICES'] = '-1'\n", "\n", "#disable warnings\n", "import warnings\n", "warnings.filterwarnings('ignore')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "In this example we will use a system of two peptides which are 12 amino acids long. First we need to create the non-mass weighted mapping operator to CG the AA trajectory. Note that the mapping operator is defined only for one peptide as the peptides are identical. " ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "Mapping operator: [[1. 1. 1. ... 0. 0. 0.]\n", " [0. 0. 0. ... 0. 0. 0.]\n", " [0. 0. 0. ... 0. 0. 0.]\n", " ...\n", " [0. 0. 0. ... 0. 0. 0.]\n", " [0. 0. 0. ... 0. 0. 0.]\n", " [0. 0. 0. ... 1. 1. 1.]]\n" ] } ], "source": [ "u = mda.Universe('test_topol.pdb','test_traj.trr')\n", "\n", "# we select segment A to define the mapping operator. \n", "segA = u.select_atoms('segid A')\n", "\n", "m = len(segA.atoms.residues) #N = num of CG beads\n", "n = len(segA.atoms) #AA = num of all atoms\n", "map_mat = np.zeros((m,n))\n", "\n", "atm_list = list(segA.atoms)\n", "for a in atm_list:\n", " cgid = a.resid\n", " aaid = a.id\n", " #print(cgid,aaid)\n", " map_mat[cgid-1,aaid-1] =1\n", "\n", "print('Mapping operator:', map_mat)\n", " " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Next we need to define the CG mapping for our system using the mappng operator above. We will use the AA topology (PDB converted into a GSD file) for this. Take a look at `example 02` for a detailed description." ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "HOOMD-blue 2.9.3 DOUBLE HPMC_MIXED TBB SSE SSE2 SSE3 \n", "Compiled: 10/17/2020\n", "Copyright (c) 2009-2019 The Regents of the University of Michigan.\n", "-----\n", "You are using HOOMD-blue. Please cite the following:\n", "* J A Anderson, J Glaser, and S C Glotzer. \"HOOMD-blue: A Python package for\n", " high-performance molecular dynamics and hard particle Monte Carlo\n", " simulations\", Computational Materials Science 173 (2020) 109363\n", "-----\n", "HOOMD-blue is running on the CPU\n", "notice(2): Group \"all\" created containing 366 particles\n", "Finding molecules...50.00%\n", "atoms per mol 183 mapping mat (12, 183)\n" ] } ], "source": [ "c = hoomd.context.initialize('--mode=cpu')\n", "system = hoomd.init.read_gsd(filename='test_topol.gsd')\n", "c.sorter.disable()\n", "set_rcut = 10.0\n", "\n", "outfile = 'testtraj_mapped.gsd'\n", "\n", "molecule_mapping_index = htf.find_molecules(system) \n", "\n", "# get number of atoms\n", "N = sum([len(m) for m in molecule_mapping_index]) \n", "\n", "# get number of molecules\n", "M = len(molecule_mapping_index) \n", "\n", "# get number of atoms in a molecule=MN\n", "MN = len(molecule_mapping_index[0])\n", "\n", "molecule_mapping = map_mat\n", "print('atoms per mol',MN,'mapping mat',molecule_mapping.shape)\n", "bead_number = molecule_mapping.shape[0]\n", "\n", "cg_mapping = htf.sparse_mapping([molecule_mapping for _ in molecule_mapping_index], \n", " molecule_mapping_index, system=system)\n", "\n", "assert cg_mapping.shape == (M * bead_number, N)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "Now let's read the trajectory and generate CG bead types, indices and COMs. There are 24 residues in the system. Hence we will name each bead index by an integer scaling from 1 to 24. CG beads names will be `B + index`. A user can give any bead name of choice. We will write each mapped state to the output file in GSD format." ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stderr", "output_type": "stream", "text": [ " 3%|▎ | 26/801 [00:00<00:02, 259.66it/s]" ] }, { "name": "stdout", "output_type": "stream", "text": [ "Number of CG beads: 24\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "100%|██████████| 801/801 [00:01<00:00, 635.23it/s]" ] }, { "name": "stdout", "output_type": "stream", "text": [ "GSD file written\n" ] }, { "name": "stderr", "output_type": "stream", "text": [ "\n" ] } ], "source": [ "t = gsd.hoomd.open(name=outfile, mode='wb')\n", "frame_num = 0\n", "\n", "CGnum = M * bead_number\n", "print('Number of CG beads: ',CGnum)\n", "CGids = np.arange(1,CGnum+1)\n", "\n", "#creating bead names\n", "CGtypes = []\n", "for i in CGids:\n", " CGtypes.append('B'+str(i))\n", "\n", "for inputs, ts in htf.iter_from_trajectory(16, u, r_cut=45):\n", " positions = inputs[1]\n", " box = inputs[2]\n", " box_size = htf.box_size(box)\n", " positions = positions[:, :3]\n", " \n", " # First let's calculate the COMs of the CG groups\n", " #Note that each residue is grouped into one atom group and its COM is computed\n", " \n", " mapped_pos = htf.center_of_mass(tf.cast(positions[:,:3],dtype=tf.float64), \n", " tf.cast(cg_mapping,dtype=tf.float64), box_size)\n", " mdbox = u.dimensions\n", " coms = mapped_pos.numpy()\n", " \n", " #Let's generate snapshots of each frame and write to a GSD file \n", " t.append(htf.create_frame(frame_num, CGnum, CGtypes, CGids, coms, mdbox))\n", " frame_num += 1\n", "\n", "print('GSD file written') " ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "To see test if our mapped trajectory was written properly, we can try and read the `CG_tutorial/testtraj_mapped.gsd` file. You can see how the position of the first CG bead changes over the frames. " ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ "0 [ 35.35711 -27.433498 -7.809485]\n", "1 [-34.50918 -27.639172 -8.4015665]\n", "2 [ 34.66662 -27.38856 -8.202412]\n", "3 [-35.01347 -28.389769 -9.379036]\n", "4 [ 35.357594 -28.340115 -8.737451]\n", "5 [ 35.06292 -28.791862 -7.920139]\n", "6 [ 35.12232 -28.025568 -8.438357]\n", "7 [-34.709858 -28.492348 -7.9871583]\n", "8 [-34.16562 -27.651974 -8.296957]\n", "9 [-34.01467 -27.425991 -8.542728]\n", "10 [-34.589207 -26.794699 -7.9599514]\n", "11 [-33.7034 -27.556913 -6.724072]\n", "12 [-32.954582 -27.075233 -7.6588087]\n", "13 [-33.3348 -26.861336 -8.06112 ]\n", "14 [-34.122303 -28.119959 -7.858933]\n", "15 [-33.932766 -27.566809 -8.017298]\n", "16 [-34.707756 -27.124765 -9.155902]\n", "17 [ 34.312122 -26.923996 -8.485293]\n", "18 [ 34.638252 -26.665678 -8.7566805]\n", "19 [ 35.307434 -26.312263 -8.163395]\n", "20 [-35.434082 -26.071924 -8.643723]\n", "21 [-35.16003 -26.542374 -8.962957]\n", "22 [-34.137714 -26.128155 -8.694891]\n", "23 [ 35.15582 -25.390306 -9.582587]\n", "24 [ 35.094425 -25.399876 -8.848779]\n", "25 [ 35.143196 -25.233618 -7.952073]\n", "26 [ 35.12159 -24.783445 -7.4388504]\n", "27 [ 35.332157 -25.096634 -7.4453654]\n", "28 [-35.11884 -25.190023 -7.192968]\n", "29 [-34.7561 -25.367384 -7.546586]\n", "30 [-34.961823 -25.736475 -6.9259343]\n", "31 [-34.065468 -25.38594 -7.0923295]\n", "32 [-34.632504 -25.390774 -6.811906]\n", "33 [-33.8376 -24.8596 -7.8718123]\n", "34 [-34.46248 -24.764788 -8.434978]\n", "35 [ 35.340355 -24.249422 -9.075802]\n", "36 [-35.299095 -23.714283 -9.522739]\n", "37 [-34.275112 -24.008446 -10.465595]\n", "38 [-33.33931 -24.840975 -9.53776 ]\n", "39 [-34.406925 -24.23184 -10.301131]\n", "40 [-33.728218 -24.715237 -10.657242]\n", "41 [-33.995556 -25.225674 -10.417688]\n", "42 [-34.416878 -25.149817 -11.122389]\n", "43 [-34.9447 -24.931875 -11.2053 ]\n", "44 [-35.426777 -25.675413 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32.009743 -25.739197 ]\n", "786 [ 14.267766 33.078552 -25.637243]\n", "787 [ 14.987862 33.966015 -25.624584]\n", "788 [ 15.17325 33.3548 -24.726744]\n", "789 [ 14.660181 33.719337 -24.525137]\n", "790 [ 14.391443 34.03137 -25.056479]\n", "791 [ 15.438659 33.14854 -24.699305]\n", "792 [ 14.944542 34.23818 -25.79746 ]\n", "793 [ 13.913737 34.086132 -25.977367]\n", "794 [ 12.563915 34.84776 -28.200745]\n", "795 [ 11.749745 34.36046 -28.21888 ]\n", "796 [ 11.906162 34.27409 -28.236387]\n", "797 [ 11.573023 34.800217 -28.36714 ]\n", "798 [ 10.603988 33.988716 -27.779749]\n", "799 [ 10.839826 33.375492 -28.480227]\n", "800 [ 10.742377 33.4503 -27.918385]\n" ] } ], "source": [ "with gsd.pygsd.GSDFile(open(outfile, 'rb')) as f:\n", " t = gsd.hoomd.HOOMDTrajectory(f)\n", " for frame,i in enumerate(t):\n", " pos = i.particles.position\n", " types = i.particles.types\n", " typeids = i.particles.typeid\n", " print(frame, pos[0])" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3", "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": "3.8.5" } }, "nbformat": 4, "nbformat_minor": 4 }