diff --git a/notebooks/experiments/experiment_k2/gpt-4o-2024-05-13/exp_20.ipynb b/notebooks/experiments/experiment_k2/gpt-4o-2024-05-13/exp_20.ipynb new file mode 100644 index 00000000..c29a3c5f --- /dev/null +++ b/notebooks/experiments/experiment_k2/gpt-4o-2024-05-13/exp_20.ipynb @@ -0,0 +1,719 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import datetime\n", + "import os\n", + "from mdagent import MDAgent\n", + "import matplotlib.pyplot as plt" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "date and time: 2024-07-25\n", + "time: 15:51:02\n", + "LLM: gpt-4o-2024-05-13 \n", + "Temperature: 0.1\n" + ] + } + ], + "source": [ + "prompt20 = \"Simulate 1MBN in water and in methanol solutions.\"\n", + "llm_var = \"gpt-4o-2024-05-13\"\n", + "tools = \"all\"\n", + "agent = MDAgent(agent_type=\"Structured\", model=llm_var, top_k_tools=tools)\n", + "now = datetime.datetime.now()\n", + "date = now.strftime(\"%Y-%m-%d\")\n", + "print(\"date and time:\",date)\n", + "time = now.strftime(\"%H:%M:%S\")\n", + "print(\"time:\",time)\n", + "print(\"LLM: \",agent.llm.model_name,\"\\nTemperature: \",agent.llm.temperature)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Thought: To simulate the protein 1MBN in both water and methanol solutions, I need to set up two separate simulations. First, I will download the PDB file for 1MBN. Then, I will create two different simulation environments: one with water and one with methanol. Finally, I will run the simulations for both environments.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"PDBFileDownloader\",\n", + " \"action_input\": \"1MBN\"\n", + "}\n", + "```PDB file found with this ID: 1MBN\n" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "2024-07-25 15:51:05.757 \n", + " \u001b[33m\u001b[1mWarning:\u001b[0m to view this Streamlit app on a browser, run it with the following\n", + " command:\n", + "\n", + " streamlit run /scratch/qcampbe2/myenvs/mdagent/lib/python3.12/site-packages/ipykernel_launcher.py [ARGUMENTS]\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "To proceed with the simulation of 1MBN in both water and methanol solutions, I need to set up the simulation environments. I will use the `packmol_tool` to create the boxes for both water and methanol solutions. \n", + "\n", + "First, I will create the box for the water solution.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"packmol_tool\",\n", + " \"action_input\": {\n", + " \"pdbfiles_id\": [\"1MBN_155105\"],\n", + " \"small_molecules\": [\"water\"],\n", + " \"number_of_molecules\": [1, 1000],\n", + " \"instructions\": [\n", + " [\"fixed 0. 0. 0. 0. 0. 0. centerofmass\"],\n", + " [\"inside box 0. 0. 0. 90. 90. 90.\"]\n", + " ]\n", + " }\n", + "}\n", + "```" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[15:51:09] SMILES Parse Error: syntax error while parsing: water\n", + "[15:51:09] SMILES Parse Error: Failed parsing SMILES 'water' for input: 'water'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "962\n", + "finished writing pdb file\n", + "Starting Packmol Tool!\n", + "Small molecules PDBs created successfully\n", + "Packing: Packed Structures of the following molecules:\n", + "Molecule ID: 1MBN_155105, Number of Molecules: 1\n", + "Molecule ID: water, Number of Molecules: 1000 \n", + "The file name is: 1_1MBN_155105_and_1000_water_v1.pdb\n", + "[!] Line 1 is short: 1 < 80\n", + "[!] Line 2 is short: 1 < 80\n", + "[!] Line 3 is short: 1 < 80\n", + "[!] Line 4 is short: 1 < 80\n", + "[!] Line 5 is short: 1 < 80\n", + "[!] Line 6 is short: 1 < 80\n", + "[!] Line 7 is short: 1 < 80\n", + "[!] Line 8 is short: 1 < 80\n", + "[!] Line 9 is short: 1 < 80\n", + "[!] Line 10 is short: 1 < 80\n", + "[!] Line 11 is short: 1 < 80\n", + "[!] Line 12 is short: 1 < 80\n", + "[!] Line 13 is short: 1 < 80\n", + "[!] Line 14 is short: 1 < 80\n", + "[!] Line 15 is short: 1 < 80\n", + "[!] Line 16 is short: 1 < 80\n", + "[!] Line 17 is short: 1 < 80\n", + "[!] Line 18 is short: 1 < 80\n", + "[!] Line 19 is short: 1 < 80\n", + "[!] Line 20 is short: 1 < 80\n", + "[!] Line 21 is short: 1 < 80\n", + "[!] Line 22 is short: 1 < 80\n", + "[!] Line 23 is short: 1 < 80\n", + "[!] Line 24 is short: 1 < 80\n", + "[!] Line 25 is short: 1 < 80\n", + "[!] Line 26 is short: 1 < 80\n", + "[!] Line 27 is short: 1 < 80\n", + "[!] Line 28 is short: 1 < 80\n", + "[!] Line 29 is short: 1 < 80\n", + "[!] Line 30 is short: 1 < 80\n", + "[!] Line 31 is short: 1 < 80\n", + "[!] Line 32 is short: 1 < 80\n", + "[!] Line 33 is short: 1 < 80\n", + "[!] Line 34 is short: 1 < 80\n", + "[!] Line 35 is short: 1 < 80\n", + "successfull!\n", + "To continue with the simulation setup, I need to create the box for the methanol solution using the `packmol_tool`. \n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"packmol_tool\",\n", + " \"action_input\": {\n", + " \"pdbfiles_id\": [\"1MBN_155105\"],\n", + " \"small_molecules\": [\"methanol\"],\n", + " \"number_of_molecules\": [1, 1000],\n", + " \"instructions\": [\n", + " [\"fixed 0. 0. 0. 0. 0. 0. centerofmass\"],\n", + " [\"inside box 0. 0. 0. 90. 90. 90.\"]\n", + " ]\n", + " }\n", + "}\n", + "```" + ] + }, + { + "name": "stderr", + "output_type": "stream", + "text": [ + "[15:51:13] SMILES Parse Error: syntax error while parsing: methanol\n", + "[15:51:13] SMILES Parse Error: Failed parsing SMILES 'methanol' for input: 'methanol'\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "887\n", + "finished writing pdb file\n", + "Starting Packmol Tool!\n", + "Small molecules PDBs created successfully\n", + "Packing: Packed Structures of the following molecules:\n", + "Molecule ID: 1MBN_155105, Number of Molecules: 1\n", + "Molecule ID: methanol, Number of Molecules: 1000 \n", + "The file name is: 1_1MBN_155105_and_1000_methanol_v1.pdb\n", + "[!] Line 1 is short: 1 < 80\n", + "[!] Line 2 is short: 1 < 80\n", + "[!] Line 3 is short: 1 < 80\n", + "[!] Line 4 is short: 1 < 80\n", + "[!] Line 5 is short: 1 < 80\n", + "[!] Line 6 is short: 1 < 80\n", + "[!] Line 7 is short: 1 < 80\n", + "[!] Line 8 is short: 1 < 80\n", + "[!] Line 9 is short: 1 < 80\n", + "[!] Line 10 is short: 1 < 80\n", + "[!] Line 11 is short: 1 < 80\n", + "[!] Line 12 is short: 1 < 80\n", + "[!] Line 13 is short: 1 < 80\n", + "[!] Line 14 is short: 1 < 80\n", + "[!] Line 15 is short: 1 < 80\n", + "[!] Line 16 is short: 1 < 80\n", + "[!] Line 17 is short: 1 < 80\n", + "[!] Line 18 is short: 1 < 80\n", + "[!] Line 19 is short: 1 < 80\n", + "[!] Line 20 is short: 1 < 80\n", + "[!] Line 21 is short: 1 < 80\n", + "[!] Line 22 is short: 1 < 80\n", + "[!] Line 23 is short: 1 < 80\n", + "[!] Line 24 is short: 1 < 80\n", + "[!] Line 25 is short: 1 < 80\n", + "[!] Line 26 is short: 1 < 80\n", + "[!] Line 27 is short: 1 < 80\n", + "[!] Line 28 is short: 1 < 80\n", + "[!] Line 29 is short: 1 < 80\n", + "[!] Line 30 is short: 1 < 80\n", + "[!] Line 31 is short: 1 < 80\n", + "[!] Line 32 is short: 1 < 80\n", + "[!] Line 33 is short: 1 < 80\n", + "[!] Line 34 is short: 1 < 80\n", + "[!] Line 35 is short: 1 < 80\n", + "[!] Line 36 is short: 1 < 80\n", + "[!] Line 37 is short: 1 < 80\n", + "[!] Line 38 is short: 1 < 80\n", + "successfull!\n", + "To proceed with the simulation of 1MBN in both water and methanol solutions, I need to set up and run the simulations for both environments. I will use the `SetUpandRunFunction` tool to set up and run the simulations.\n", + "\n", + "First, I will set up and run the simulation for the water solution.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"SetUpandRunFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"PACKED_155110\",\n", + " \"forcefield_files\": [],\n", + " \"save\": true,\n", + " \"system_params\": {\n", + " \"nonbondedMethod\": \"PME\",\n", + " \"nonbondedCutoff\": \"1 * nanometers\",\n", + " \"constraints\": \"HBonds\",\n", + " \"rigidWater\": true,\n", + " \"constraintTolerance\": 0.00001,\n", + " \"solvate\": true\n", + " },\n", + " \"integrator_params\": {\n", + " \"integrator_type\": \"LangevinMiddle\",\n", + " \"Temperature\": \"300 * kelvin\",\n", + " \"Friction\": \"1.0 / picoseconds\",\n", + " \"Timestep\": \"0.002 * picoseconds\",\n", + " \"Pressure\": \"1.0 * bar\"\n", + " },\n", + " \"simulation_params\": {\n", + " \"Ensemble\": \"NPT\",\n", + " \"Number of Steps\": 5000,\n", + " \"record_interval_steps\": 100,\n", + " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", + " }\n", + " }\n", + "}\n", + "```\n", + "Setting default ewaldErrorTolerance: 0.0005 \n", + "Setting default forcefields v2\n", + "Building system...\n", + "About to create system...\n", + "Attempts at creating system: 0/3\n", + "Error adding solvent: AttributeError – 'NoneType' object has no attribute 'value_in_unit'\n", + "Trying to add solvent with 1 nm padding\n", + "Error adding solvent ValueError – No template found for residue 1 (VAL). The set of atoms is similar to PRO, but it is missing 7 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", + "To address the issue with the missing hydrogen atoms in the residue VAL, I need to clean the PDB file to add the missing atoms and hydrogens. I will use the `CleaningToolFunction` to perform this operation on the PACKED_155110 file.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"CleaningToolFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"PACKED_155110\",\n", + " \"replace_nonstandard_residues\": true,\n", + " \"add_missing_atoms\": true,\n", + " \"remove_heterogens\": true,\n", + " \"remove_water\": false,\n", + " \"add_hydrogens\": true,\n", + " \"add_hydrogens_ph\": 7.0\n", + " }\n", + "}\n", + "```file path: /gpfs/fs2/scratch/qcampbe2/repos/md-agent/ckpt/ckpt_65/pdb/1_1MBN_155105_and_1000_water_v1.pdb\n", + "To proceed with the simulation of 1MBN in the water solution, I will now set up and run the simulation using the cleaned PDB file (1_155127).\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"SetUpandRunFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"1_155127\",\n", + " \"forcefield_files\": [],\n", + " \"save\": true,\n", + " \"system_params\": {\n", + " \"nonbondedMethod\": \"PME\",\n", + " \"nonbondedCutoff\": \"1 * nanometers\",\n", + " \"constraints\": \"HBonds\",\n", + " \"rigidWater\": true,\n", + " \"constraintTolerance\": 0.00001,\n", + " \"solvate\": true\n", + " },\n", + " \"integrator_params\": {\n", + " \"integrator_type\": \"LangevinMiddle\",\n", + " \"Temperature\": \"300 * kelvin\",\n", + " \"Friction\": \"1.0 / picoseconds\",\n", + " \"Timestep\": \"0.002 * picoseconds\",\n", + " \"Pressure\": \"1.0 * bar\"\n", + " },\n", + " \"simulation_params\": {\n", + " \"Ensemble\": \"NPT\",\n", + " \"Number of Steps\": 5000,\n", + " \"record_interval_steps\": 100,\n", + " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", + " }\n", + " }\n", + "}\n", + "```Setting default ewaldErrorTolerance: 0.0005 \n", + "Setting default forcefields v2\n", + "Building system...\n", + "About to create system...\n", + "Attempts at creating system: 0/3\n", + "Error adding solvent: AttributeError – 'NoneType' object has no attribute 'value_in_unit'\n", + "Trying to add solvent with 1 nm padding\n", + "Error adding solvent ValueError – No template found for residue 153 (GLY). The set of atoms matches GLY, but the bonds are different. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", + "To address the issue with the residue GLY, I need to ensure that all residues are correctly templated and that the PDB file is fully prepared for simulation. I will use the `CleaningToolFunction` again to ensure all residues, including GLY, are correctly handled.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"CleaningToolFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"1_155127\",\n", + " \"replace_nonstandard_residues\": true,\n", + " \"add_missing_atoms\": true,\n", + " \"remove_heterogens\": true,\n", + " \"remove_water\": false,\n", + " \"add_hydrogens\": true,\n", + " \"add_hydrogens_ph\": 7.0\n", + " }\n", + "}\n", + "```file path: /gpfs/fs2/scratch/qcampbe2/repos/md-agent/ckpt/ckpt_65/pdb/1_Clean_20240725_155127.pdb\n", + "To proceed with the simulation of 1MBN in the water solution, I will now set up and run the simulation using the newly cleaned PDB file (1_155139). If this succeeds, I will then proceed to set up and run the simulation for the methanol solution.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"SetUpandRunFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"1_155139\",\n", + " \"forcefield_files\": [],\n", + " \"save\": true,\n", + " \"system_params\": {\n", + " \"nonbondedMethod\": \"PME\",\n", + " \"nonbondedCutoff\": \"1 * nanometers\",\n", + " \"constraints\": \"HBonds\",\n", + " \"rigidWater\": true,\n", + " \"constraintTolerance\": 0.00001,\n", + " \"solvate\": true\n", + " },\n", + " \"integrator_params\": {\n", + " \"integrator_type\": \"LangevinMiddle\",\n", + " \"Temperature\": \"300 * kelvin\",\n", + " \"Friction\": \"1.0 / picoseconds\",\n", + " \"Timestep\": \"0.002 * picoseconds\",\n", + " \"Pressure\": \"1.0 * bar\"\n", + " },\n", + " \"simulation_params\": {\n", + " \"Ensemble\": \"NPT\",\n", + " \"Number of Steps\": 5000,\n", + " \"record_interval_steps\": 100,\n", + " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", + " }\n", + " }\n", + "}\n", + "```Setting default ewaldErrorTolerance: 0.0005 \n", + "Setting default forcefields v2\n", + "Building system...\n", + "About to create system...\n", + "Attempts at creating system: 0/3\n", + "Error adding solvent: AttributeError – 'NoneType' object has no attribute 'value_in_unit'\n", + "Trying to add solvent with 1 nm padding\n", + "Error adding solvent ValueError – No template found for residue 153 (GLY). The set of atoms matches GLY, but the bonds are different. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", + "To address the persistent issue with the residue GLY, I need to ensure that the PDB file is fully prepared for simulation. I will use the `CleaningToolFunction` again, but this time I will also remove water molecules to ensure no interference. After cleaning, I will attempt to set up and run the simulation again.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"CleaningToolFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"1_155139\",\n", + " \"replace_nonstandard_residues\": true,\n", + " \"add_missing_atoms\": true,\n", + " \"remove_heterogens\": true,\n", + " \"remove_water\": true,\n", + " \"add_hydrogens\": true,\n", + " \"add_hydrogens_ph\": 7.0\n", + " }\n", + "}\n", + "```file path: /gpfs/fs2/scratch/qcampbe2/repos/md-agent/ckpt/ckpt_65/pdb/1_Clean_20240725_155139.pdb\n", + "To proceed with the simulation of 1MBN in the water solution, I will now set up and run the simulation using the newly cleaned PDB file (1_155213). If this succeeds, I will then proceed to set up and run the simulation for the methanol solution.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"SetUpandRunFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"1_155213\",\n", + " \"forcefield_files\": [],\n", + " \"save\": true,\n", + " \"system_params\": {\n", + " \"nonbondedMethod\": \"PME\",\n", + " \"nonbondedCutoff\": \"1 * nanometers\",\n", + " \"constraints\": \"HBonds\",\n", + " \"rigidWater\": true,\n", + " \"constraintTolerance\": 0.00001,\n", + " \"solvate\": true\n", + " },\n", + " \"integrator_params\": {\n", + " \"integrator_type\": \"LangevinMiddle\",\n", + " \"Temperature\": \"300 * kelvin\",\n", + " \"Friction\": \"1.0 / picoseconds\",\n", + " \"Timestep\": \"0.002 * picoseconds\",\n", + " \"Pressure\": \"1.0 * bar\"\n", + " },\n", + " \"simulation_params\": {\n", + " \"Ensemble\": \"NPT\",\n", + " \"Number of Steps\": 5000,\n", + " \"record_interval_steps\": 100,\n", + " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", + " }\n", + " }\n", + "}\n", + "```Setting default ewaldErrorTolerance: 0.0005 \n", + "Setting default forcefields v2\n", + "Building system...\n", + "About to create system...\n", + "Attempts at creating system: 0/3\n", + "Error adding solvent: AttributeError – 'NoneType' object has no attribute 'value_in_unit'\n", + "Trying to add solvent with 1 nm padding\n", + "System built successfully\n", + " >\n", + "Setting up integrator...\n", + "Creating simulation...\n", + "simulation set!\n", + "Performing energy minimization...\n", + "Minimization complete!\n", + "Initial Positions saved to initial_positions.pdb\n", + "Equilibrating...\n", + "Simulating...\n", + "Done!\n", + "Standalone simulation script written to /gpfs/fs2/scratch/qcampbe2/repos/md-agent/ckpt/ckpt_65/simulations/NPT_1_155213_20240725_155219.py\n", + "['exp_10.ipynb', 'TRAJ_sim0_155435_2YXF_155429_20240725_155437.dcd', 'exp_13.ipynb', 'exp_22.ipynb', 'exp_8.ipynb', 'TOP_sim0_155219_1_155213_20240725_155223.pdb', 'exp_3.ipynb', 'exp_1.ipynb', '.ipynb_checkpoints', 'LOG_sim0_155219_1_155213_20240725_155223.txt', 'exp_4.ipynb', 'packmol.inp', 'exp_12.ipynb', 'exp_19.ipynb', 'TOP_sim0_155435_2YXF_155429_20240725_155437.pdb', 'exp_9.ipynb', 'exp_5.ipynb', 'exp_7.ipynb', 'exp_2.ipynb', 'exp_18.ipynb', 'exp_14.ipynb', 'TRAJ_sim0_155219_1_155213_20240725_155223.dcd', 'exp_6.ipynb', 'exp_20.ipynb', 'exp_11.ipynb', 'exp_21.ipynb', 'exp_25.ipynb', 'LOG_sim0_155435_2YXF_155429_20240725_155437.txt']\n", + "To proceed with the simulation of 1MBN in the methanol solution, I will now set up and run the simulation using the previously packed PDB file (PACKED_155114). \n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"SetUpandRunFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"PACKED_155114\",\n", + " \"forcefield_files\": [],\n", + " \"save\": true,\n", + " \"system_params\": {\n", + " \"nonbondedMethod\": \"PME\",\n", + " \"nonbondedCutoff\": \"1 * nanometers\",\n", + " \"constraints\": \"HBonds\",\n", + " \"rigidWater\": true,\n", + " \"constraintTolerance\": 0.00001,\n", + " \"solvate\": true\n", + " },\n", + " \"integrator_params\": {\n", + " \"integrator_type\": \"LangevinMiddle\",\n", + " \"Temperature\": \"300 * kelvin\",\n", + " \"Friction\": \"1.0 / picoseconds\",\n", + " \"Timestep\": \"0.002 * picoseconds\",\n", + " \"Pressure\": \"1.0 * bar\"\n", + " },\n", + " \"simulation_params\": {\n", + " \"Ensemble\": \"NPT\",\n", + " \"Number of Steps\": 5000,\n", + " \"record_interval_steps\": 100,\n", + " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", + " }\n", + " }\n", + "}\n", + "```\n", + "Setting default ewaldErrorTolerance: 0.0005 \n", + "Setting default forcefields v2\n", + "Building system...\n", + "About to create system...\n", + "Attempts at creating system: 0/3\n", + "Error adding solvent: AttributeError – 'NoneType' object has no attribute 'value_in_unit'\n", + "Trying to add solvent with 1 nm padding\n", + "Error adding solvent ValueError – No template found for residue 1 (VAL). The set of atoms is similar to PRO, but it is missing 7 hydrogen atoms. For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template\n", + "To address the issue with the missing hydrogen atoms in the residue VAL for the methanol solution, I need to clean the PDB file to add the missing atoms and hydrogens. I will use the `CleaningToolFunction` to perform this operation on the PACKED_155114 file.\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"CleaningToolFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"PACKED_155114\",\n", + " \"replace_nonstandard_residues\": true,\n", + " \"add_missing_atoms\": true,\n", + " \"remove_heterogens\": true,\n", + " \"remove_water\": false,\n", + " \"add_hydrogens\": true,\n", + " \"add_hydrogens_ph\": 7.0\n", + " }\n", + "}\n", + "```file path: /gpfs/fs2/scratch/qcampbe2/repos/md-agent/ckpt/ckpt_65/pdb/1_1MBN_155105_and_1000_methanol_v1.pdb\n", + "To proceed with the simulation of 1MBN in the methanol solution, I will now set up and run the simulation using the cleaned PDB file (1_155517).\n", + "\n", + "Action:\n", + "```\n", + "{\n", + " \"action\": \"SetUpandRunFunction\",\n", + " \"action_input\": {\n", + " \"pdb_id\": \"1_155517\",\n", + " \"forcefield_files\": [],\n", + " \"save\": true,\n", + " \"system_params\": {\n", + " \"nonbondedMethod\": \"PME\",\n", + " \"nonbondedCutoff\": \"1 * nanometers\",\n", + " \"constraints\": \"HBonds\",\n", + " \"rigidWater\": true,\n", + " \"constraintTolerance\": 0.00001,\n", + " \"solvate\": true\n", + " },\n", + " \"integrator_params\": {\n", + " \"integrator_type\": \"LangevinMiddle\",\n", + " \"Temperature\": \"300 * kelvin\",\n", + " \"Friction\": \"1.0 / picoseconds\",\n", + " \"Timestep\": \"0.002 * picoseconds\",\n", + " \"Pressure\": \"1.0 * bar\"\n", + " },\n", + " \"simulation_params\": {\n", + " \"Ensemble\": \"NPT\",\n", + " \"Number of Steps\": 5000,\n", + " \"record_interval_steps\": 100,\n", + " \"record_params\": [\"step\", \"potentialEnergy\", \"temperature\"]\n", + " }\n", + " }\n", + "}\n", + "```Setting default ewaldErrorTolerance: 0.0005 \n", + "Setting default forcefields v2\n", + "Building system...\n", + "About to create system...\n", + "Attempts at creating system: 0/3\n", + "Error adding solvent: AttributeError – 'NoneType' object has no attribute 'value_in_unit'\n", + "Trying to add solvent with 1 nm padding\n", + "System built successfully\n", + " >\n", + "Setting up integrator...\n", + "Creating simulation...\n", + "simulation set!\n", + "Performing energy minimization...\n", + "Minimization complete!\n", + "Initial Positions saved to initial_positions.pdb\n", + "Equilibrating...\n", + "Simulating...\n", + "Done!\n", + "Standalone simulation script written to /gpfs/fs2/scratch/qcampbe2/repos/md-agent/ckpt/ckpt_65/simulations/NPT_1_155517_20240725_155532.py\n", + "['exp_10.ipynb', 'TRAJ_sim0_155435_2YXF_155429_20240725_155437.dcd', 'exp_13.ipynb', 'exp_22.ipynb', 'exp_8.ipynb', 'LOG_sim0_155532_1_155517_20240725_155535.txt', 'TRAJ_sim0_155532_1_155517_20240725_155535.dcd', 'exp_3.ipynb', 'exp_1.ipynb', '.ipynb_checkpoints', 'exp_4.ipynb', 'packmol.inp', 'TOP_sim0_155532_1_155517_20240725_155535.pdb', 'exp_12.ipynb', 'exp_19.ipynb', 'TOP_sim0_155435_2YXF_155429_20240725_155437.pdb', 'exp_9.ipynb', 'exp_5.ipynb', 'exp_7.ipynb', 'exp_2.ipynb', 'exp_18.ipynb', 'exp_14.ipynb', 'exp_6.ipynb', 'exp_20.ipynb', 'exp_11.ipynb', 'exp_21.ipynb', 'exp_25.ipynb', 'LOG_sim0_155435_2YXF_155429_20240725_155437.txt']\n", + "Both simulations for 1MBN in water and methanol solutions have been successfully completed. Here are the details:\n", + "\n", + "### Simulation in Water Solution:\n", + "- **PDB File ID:** 1_155213\n", + "- **Simulation Summary:**\n", + " - **Trajectory File:** rec0_155223\n", + " - **State Log File:** rec1_155223\n", + " - **PDB Frames File:** rec2_155223\n", + "- **Standalone Script ID:** sim0_155219\n", + "- **Initial Topology File ID:** top_sim0_155219\n", + "\n", + "### Simulation in Methanol Solution:\n", + "- **PDB File ID:** 1_155517\n", + "- **Simulation Summary:**\n", + " - **Trajectory File:** rec0_155535\n", + " - **State Log File:** rec1_155535\n", + " - **PDB Frames File:** rec2_155535\n", + "- **Standalone Script ID:** sim0_155532\n", + "- **Initial Topology File ID:** top_sim0_155532\n", + "\n", + "You can use the provided file IDs to access the simulation results and further analyze the behavior of 1MBN in both water and methanol solutions.\n", + "\n", + "Final Answer: The simulations of 1MBN in both water and methanol solutions have been successfully completed. The details and file IDs for accessing the simulation results are provided above.The agent successfully completed simulations of 1MBN in both water and methanol solutions. The simulation in water solution had a PDB File ID of 1_155213, with trajectory, state log, and PDB frames files labeled as rec0_155223, rec1_155223, and rec2_155223 respectively. The standalone script ID was sim0_155219, and the initial topology file ID was top_sim0_155219.\n", + "\n", + "Similarly, the simulation in methanol solution had a PDB File ID of 1_155517, with trajectory, state log, and PDB frames files labeled as rec0_155535, rec1_155535, and rec2_155535 respectively. The standalone script ID was sim0_155532, and the initial topology file ID was top_sim0_155532.\n", + "\n", + "The agent can use the provided file IDs to access the simulation results and further analyze the behavior of 1MBN in both water and methanol solutions. The final solution indicates the successful completion of the simulations.Your run id is: 3ONXCN2N\n" + ] + }, + { + "data": { + "text/plain": [ + "('Both simulations for 1MBN in water and methanol solutions have been successfully completed. Here are the details:\\n\\n### Simulation in Water Solution:\\n- **PDB File ID:** 1_155213\\n- **Simulation Summary:**\\n - **Trajectory File:** rec0_155223\\n - **State Log File:** rec1_155223\\n - **PDB Frames File:** rec2_155223\\n- **Standalone Script ID:** sim0_155219\\n- **Initial Topology File ID:** top_sim0_155219\\n\\n### Simulation in Methanol Solution:\\n- **PDB File ID:** 1_155517\\n- **Simulation Summary:**\\n - **Trajectory File:** rec0_155535\\n - **State Log File:** rec1_155535\\n - **PDB Frames File:** rec2_155535\\n- **Standalone Script ID:** sim0_155532\\n- **Initial Topology File ID:** top_sim0_155532\\n\\nYou can use the provided file IDs to access the simulation results and further analyze the behavior of 1MBN in both water and methanol solutions.\\n\\nFinal Answer: The simulations of 1MBN in both water and methanol solutions have been successfully completed. The details and file IDs for accessing the simulation results are provided above.',\n", + " '3ONXCN2N')" + ] + }, + "execution_count": 3, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "agent.run(prompt20)" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "date and time: 2024-07-25\n", + "time: 15:59:38\n", + "Files found in registry: 1MBN_155105: PDB file downloaded from RSCB\n", + " PDBFile ID: 1MBN_155105\n", + " water: pdb file for the small molecule water\n", + " PACKED_155110: Packed Structures of the following molecules:\n", + "Molecule ID: 1MBN_155105\n", + " Number of Molecules: 1\n", + "Molecule ID: water\n", + " Number of Molecules: 1000\n", + " methanol: pdb file for the small molecule methanol\n", + " PACKED_155114: Packed Structures of the following molecules:\n", + "Molecule ID: 1MBN_155105\n", + " Number of Molecules: 1\n", + "Molecule ID: methanol\n", + " Number of Molecules: 1000\n", + " 1_155127: Cleaned File: Removed Heterogens\n", + " and Water Kept. Replaced Nonstandard Residues. Added Hydrogens at pH 7.0. Missing Atoms Added and replaces nonstandard residues. \n", + " 1_155139: Cleaned File: Removed Heterogens\n", + " and Water Kept. Replaced Nonstandard Residues. Added Hydrogens at pH 7.0. Missing Atoms Added and replaces nonstandard residues. \n", + " 1_155213: Cleaned File: Removed Heterogens\n", + " and Water Removed. Replaced Nonstandard Residues. Added Hydrogens at pH 7.0. Missing Atoms Added and replaces nonstandard residues. \n", + " top_sim0_155219: Initial positions for simulation sim0_155219\n", + " sim0_155219: Basic Simulation of Protein 1_155213\n", + " rec0_155223: Simulation trajectory for protein 1_155213 and simulation sim0_155219\n", + " rec1_155223: Simulation state log for protein 1_155213 and simulation sim0_155219\n", + " rec2_155223: Simulation pdb frames for protein 1_155213 and simulation sim0_155219\n", + " 1_155517: Cleaned File: Removed Heterogens\n", + " and Water Kept. Replaced Nonstandard Residues. Added Hydrogens at pH 7.0. Missing Atoms Added and replaces nonstandard residues. \n", + " top_sim0_155532: Initial positions for simulation sim0_155532\n", + " sim0_155532: Basic Simulation of Protein 1_155517\n", + " rec0_155535: Simulation trajectory for protein 1_155517 and simulation sim0_155532\n", + " rec1_155535: Simulation state log for protein 1_155517 and simulation sim0_155532\n", + " rec2_155535: Simulation pdb frames for protein 1_155517 and simulation sim0_155532\n" + ] + } + ], + "source": [ + "now = datetime.datetime.now()\n", + "date = now.strftime(\"%Y-%m-%d\")\n", + "print(\"date and time:\",date)\n", + "time = now.strftime(\"%H:%M:%S\")\n", + "print(\"time:\",time)\n", + "registry = agent.path_registry\n", + "paths_and_descriptions = registry.list_path_names_and_descriptions()\n", + "print(\"\\n\".join(paths_and_descriptions.split(\",\")))" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "# Experiment Result:\n", + "### Completed without Exception or TimeOut Errors ✅\n", + "### Attempted all necessary steps ✅\n", + "### Completed without hallucination ✅\n", + "### Logic make sense ✅\n", + "### Correct Answer ✅" + ] + }, + { + "cell_type": "code", + "execution_count": null, + "metadata": {}, + "outputs": [], + "source": [] + } + ], + "metadata": { + "kernelspec": { + "display_name": "mdagent", + "language": "python", + "name": "mdagent" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.12.4" + } + }, + "nbformat": 4, + "nbformat_minor": 4 +}