From cfa59271c80a73bda17c3782592eb8cae541ae32 Mon Sep 17 00:00:00 2001 From: pinyili2 <pinyili2@illinois.edu> Date: Wed, 26 Jun 2024 16:57:49 -0500 Subject: [PATCH] same as above --- .../3-run-and-customized-checkpoint.ipynb | 128 +++++++++++------- 3-run-and-customized.ipynb | 128 +++++++++++------- 2 files changed, 152 insertions(+), 104 deletions(-) diff --git a/.ipynb_checkpoints/3-run-and-customized-checkpoint.ipynb b/.ipynb_checkpoints/3-run-and-customized-checkpoint.ipynb index e8ee5f1..670aa50 100644 --- a/.ipynb_checkpoints/3-run-and-customized-checkpoint.ipynb +++ b/.ipynb_checkpoints/3-run-and-customized-checkpoint.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "fba6117b", + "id": "024005b4", "metadata": {}, "source": [ "# Learn to run simulation and implement customized coarsed-grained polymer models\n", @@ -10,23 +10,94 @@ "As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd! \n", "We will constructing a polymer model by coarse-graining the HpsModel.\n", "\n", - "## Step 1: Model Construction testing\n", + "## Step 1: Model Construction\n", "\n", - "We will begin with " + "We will start with the Hps Model we just saw in section 2 following and run the initial conformation with the same procedures. " ] }, { "cell_type": "code", "execution_count": null, - "id": "60d287ac", + "id": "04d59bef", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", + "from pathlib import Path\n", + "from arbdmodel import ArbdEngine\n", + "from arbdmodel.coords import readArbdCoords\n", "from arbdmodel.polymer import PolymerSection\n", "from arbdmodel.hps_polymer_model import _types\n", "from arbdmodel.hps_polymer_model import HpsModel as NupModel\n", "\n", + "#from info import NupModel, create_arbd_polymer_objects, dimensions\n", + "\n", + "temperature = 298.15\n", + "ion_concentration = 250 # in mM\n", + "gpu = 0\n", + "\n", + "decomp_period = 50\n", + "skin_depth = 8\n", + "## 3.2\n", + "\n", + "model_name = 'HPS'\n", + "step = 1\n", + "\n", + "## units \"sqrt(80 epsilon0 k K /(2 * (mM/particle) * e**2))\" AA\n", + "debye_length = 10\n", + "\n", + "polymers, sequences = create_arbd_polymer_objects()\n", + "\n", + "model = NupModel( polymers, sequences,\n", + " debye_length = debye_length,\n", + " temperature=temperature,\n", + " damping_coefficient = 50000, # units of 1/ns\n", + " decomp_period = decomp_period,\n", + " pairlist_distance = 50+skin_depth,\n", + " dimensions = dimensions\n", + " )\n", + "engine = ArbdEngine( integrator = 'Langevin',\n", + " num_steps=1e7,\n", + " output_period=1e4,\n", + " gpu = 0\n", + " )\n", + "directory = f'1-one_bead_per_res-{model_name}'\n", + "outname = 'run'\n", + "\n", + "if not Path(f'{directory}/output/{outname}.dcd').exists():\n", + " # \"\"\" \"Minimization\" \"\"\"\n", + " # add_restraints(model,restraints)\n", + " # model.simulate(output_name='{}-min-{}'.format(model_name,step),\n", + " # num_steps=1e3, output_period=500,\n", + " # gpu=gpu,\n", + " # )\n", + " # coords = readArbdCoords('output/{}-min-{}.restart'.format(model_name,step))\n", + " # model.update_splines(coords)\n", + "\n", + " \"\"\" Production \"\"\"\n", + " model.set_damping_coefficient( 100 )\n", + " engine.simulate(model, output_name=outname,\n", + " directory = directory\n", + " )\n" + ] + }, + { + "cell_type": "markdown", + "id": "5fb80332", + "metadata": {}, + "source": [ + "Then we can run the simulation with " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "28a28e18", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "\n", "_seq = 'GLFG' * 8 # 10 repeats per polymer\n", "## We're going to tile polymers along x and y in a square lattice\n", "Nx = 5\n", @@ -64,57 +135,10 @@ "\n" ] }, - { - "cell_type": "markdown", - "id": "e0987f4a", - "metadata": {}, - "source": [ - "Then we can run the simulation with " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1ad8de8d", - "metadata": {}, - "outputs": [], - "source": [ - "from pathlib import Path\n", - "from arbdmodel import ArbdEngine\n", - "from arbdmodel.coords import readArbdCoords\n", - "\n", - "#from info import NupModel, create_arbd_polymer_objects, dimensions\n", - "\n", - "temperature = 298.15\n", - "ion_concentration = 250 # in mM\n", - "gpu = 0\n", - "\n", - "decomp_period = 50\n", - "skin_depth = 8\n", - "## 3.2\n", - "\n", - "model_name = 'HPS'\n", - "step = 1\n", - "\n", - "## units \"sqrt(80 epsilon0 k K /(2 * (mM/particle) * e**2))\" AA\n", - "debye_length = 10\n", - "\n", - "polymers, sequences = create_arbd_polymer_objects()\n", - "\n", - "model = NupModel( polymers, sequences,\n", - " debye_length = debye_length,\n", - " temperature=temperature,\n", - " damping_coefficient = 50000, # units of 1/ns\n", - " decomp_period = decomp_period,\n", - " pairlist_distance = 50+skin_depth,\n", - " dimensions = dimensions\n", - " )\n" - ] - }, { "cell_type": "code", "execution_count": null, - "id": "6942a0b7", + "id": "b5aef887", "metadata": {}, "outputs": [], "source": [] diff --git a/3-run-and-customized.ipynb b/3-run-and-customized.ipynb index e8ee5f1..670aa50 100644 --- a/3-run-and-customized.ipynb +++ b/3-run-and-customized.ipynb @@ -2,7 +2,7 @@ "cells": [ { "cell_type": "markdown", - "id": "fba6117b", + "id": "024005b4", "metadata": {}, "source": [ "# Learn to run simulation and implement customized coarsed-grained polymer models\n", @@ -10,23 +10,94 @@ "As we've dived into the polymer objects in arbd and learned the basic usage of arbd, now it's time to put everything together and run coarsed-grained protein model using arbd! \n", "We will constructing a polymer model by coarse-graining the HpsModel.\n", "\n", - "## Step 1: Model Construction testing\n", + "## Step 1: Model Construction\n", "\n", - "We will begin with " + "We will start with the Hps Model we just saw in section 2 following and run the initial conformation with the same procedures. " ] }, { "cell_type": "code", "execution_count": null, - "id": "60d287ac", + "id": "04d59bef", "metadata": {}, "outputs": [], "source": [ "import numpy as np\n", + "from pathlib import Path\n", + "from arbdmodel import ArbdEngine\n", + "from arbdmodel.coords import readArbdCoords\n", "from arbdmodel.polymer import PolymerSection\n", "from arbdmodel.hps_polymer_model import _types\n", "from arbdmodel.hps_polymer_model import HpsModel as NupModel\n", "\n", + "#from info import NupModel, create_arbd_polymer_objects, dimensions\n", + "\n", + "temperature = 298.15\n", + "ion_concentration = 250 # in mM\n", + "gpu = 0\n", + "\n", + "decomp_period = 50\n", + "skin_depth = 8\n", + "## 3.2\n", + "\n", + "model_name = 'HPS'\n", + "step = 1\n", + "\n", + "## units \"sqrt(80 epsilon0 k K /(2 * (mM/particle) * e**2))\" AA\n", + "debye_length = 10\n", + "\n", + "polymers, sequences = create_arbd_polymer_objects()\n", + "\n", + "model = NupModel( polymers, sequences,\n", + " debye_length = debye_length,\n", + " temperature=temperature,\n", + " damping_coefficient = 50000, # units of 1/ns\n", + " decomp_period = decomp_period,\n", + " pairlist_distance = 50+skin_depth,\n", + " dimensions = dimensions\n", + " )\n", + "engine = ArbdEngine( integrator = 'Langevin',\n", + " num_steps=1e7,\n", + " output_period=1e4,\n", + " gpu = 0\n", + " )\n", + "directory = f'1-one_bead_per_res-{model_name}'\n", + "outname = 'run'\n", + "\n", + "if not Path(f'{directory}/output/{outname}.dcd').exists():\n", + " # \"\"\" \"Minimization\" \"\"\"\n", + " # add_restraints(model,restraints)\n", + " # model.simulate(output_name='{}-min-{}'.format(model_name,step),\n", + " # num_steps=1e3, output_period=500,\n", + " # gpu=gpu,\n", + " # )\n", + " # coords = readArbdCoords('output/{}-min-{}.restart'.format(model_name,step))\n", + " # model.update_splines(coords)\n", + "\n", + " \"\"\" Production \"\"\"\n", + " model.set_damping_coefficient( 100 )\n", + " engine.simulate(model, output_name=outname,\n", + " directory = directory\n", + " )\n" + ] + }, + { + "cell_type": "markdown", + "id": "5fb80332", + "metadata": {}, + "source": [ + "Then we can run the simulation with " + ] + }, + { + "cell_type": "code", + "execution_count": null, + "id": "28a28e18", + "metadata": {}, + "outputs": [], + "source": [ + "\n", + "\n", "_seq = 'GLFG' * 8 # 10 repeats per polymer\n", "## We're going to tile polymers along x and y in a square lattice\n", "Nx = 5\n", @@ -64,57 +135,10 @@ "\n" ] }, - { - "cell_type": "markdown", - "id": "e0987f4a", - "metadata": {}, - "source": [ - "Then we can run the simulation with " - ] - }, - { - "cell_type": "code", - "execution_count": null, - "id": "1ad8de8d", - "metadata": {}, - "outputs": [], - "source": [ - "from pathlib import Path\n", - "from arbdmodel import ArbdEngine\n", - "from arbdmodel.coords import readArbdCoords\n", - "\n", - "#from info import NupModel, create_arbd_polymer_objects, dimensions\n", - "\n", - "temperature = 298.15\n", - "ion_concentration = 250 # in mM\n", - "gpu = 0\n", - "\n", - "decomp_period = 50\n", - "skin_depth = 8\n", - "## 3.2\n", - "\n", - "model_name = 'HPS'\n", - "step = 1\n", - "\n", - "## units \"sqrt(80 epsilon0 k K /(2 * (mM/particle) * e**2))\" AA\n", - "debye_length = 10\n", - "\n", - "polymers, sequences = create_arbd_polymer_objects()\n", - "\n", - "model = NupModel( polymers, sequences,\n", - " debye_length = debye_length,\n", - " temperature=temperature,\n", - " damping_coefficient = 50000, # units of 1/ns\n", - " decomp_period = decomp_period,\n", - " pairlist_distance = 50+skin_depth,\n", - " dimensions = dimensions\n", - " )\n" - ] - }, { "cell_type": "code", "execution_count": null, - "id": "6942a0b7", + "id": "b5aef887", "metadata": {}, "outputs": [], "source": [] -- GitLab