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Jgmedina95 committed Jul 11, 2024
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94 changes: 81 additions & 13 deletions notebooks/experiments/gpt-4o-2024-05-13/exp_24.ipynb
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"Minimization complete!\n",
"Initial Positions saved to initial_positions.pdb\n",
"Equilibrating...\n",
"Simulating...\n"
"Simulating...\n",
"Done!\n",
"Standalone simulation script written to /Users/jorgemedina/Desktop/md-agent/ckpt/ckpt_107/simulations/NPT_1A3N_230519_20240710_230525.py\n",
"['TRAJ_sim0_230525_1A3N_230519_20240710_230532.dcd', 'exp_17.ipynb', 'TOP_sim0_203045_1C3W_203041_20240710_203056.pdb', 'TOP_sim0_210859_2YXF_210850_20240710_210901.pdb', 'LOG_sim0_230525_1A3N_230519_20240710_230532.txt', 'exp_8.ipynb', 'exp_4.ipynb', 'TRAJ_sim0_203045_1C3W_203041_20240710_203056.dcd', 'LOG_sim0_210859_2YXF_210850_20240710_210901.txt', 'exp_25.ipynb', 'exp_18.ipynb', 'exp_6.ipynb', 'exp_21.ipynb', 'exp_2.ipynb', 'exp_23.ipynb', 'TOP_sim0_230525_1A3N_230519_20240710_230532.pdb', 'exp_7.ipynb', 'exp_19.ipynb', 'exp_24.ipynb', 'exp_5.ipynb', 'LOG_sim0_203045_1C3W_203041_20240710_203056.txt', 'TRAJ_sim0_210859_2YXF_210850_20240710_210901.dcd', 'exp_22.ipynb', 'exp_1.ipynb', 'exp_3.ipynb', 'packmol.inp', 'exp_20.ipynb']\n",
"To analyze the radial distribution function (RDF) of the simulation of the protein 1A3N solvated in water, I now have the necessary trajectory and topology files generated from the simulation. I will use the RDFTool to perform this analysis.\n",
"\n",
"Action:\n",
"```\n",
"{\n",
" \"action\": \"RDFTool\",\n",
" \"action_input\": {\n",
" \"input\": {\n",
" \"trajectory_fileid\": \"rec0_230532\",\n",
" \"topology_fileid\": \"top_sim0_230525\"\n",
" }\n",
" }\n",
"}\n",
"```The radial distribution function (RDF) analysis for the simulation of the protein 1A3N solvated in water has been successfully completed. The RDF plot has been generated and is available for review.\n",
"\n",
"Final Answer: The RDF analysis for the simulation of the protein 1A3N solvated in water has been successfully completed. The RDF plot has been generated and saved as `fig0_231508`. This plot provides insights into the spatial distribution of water molecules around the protein, which is crucial for understanding solvation effects and protein-water interactions.Prompt: Conduct RDF analysis for the simulation of protein 1A3N solvated in water.\n",
"\n",
"Step 1: Gather simulation data for protein 1A3N solvated in water.\n",
"Step 2: Calculate pair correlation function to determine RDF.\n",
"Step 3: Generate RDF plot.\n",
"Step 4: Review and analyze RDF plot.\n",
"Step 5: Save RDF plot as `fig0_231508`.\n",
"\n",
"Final Solution: The RDF analysis for the simulation of the protein 1A3N solvated in water has been successfully completed. The RDF plot has been generated and saved as `fig0_231508`. This plot provides insights into the spatial distribution of water molecules around the protein, which is crucial for understanding solvation effects and protein-water interactions.Your run id is: 5I7VMFV0\n"
]
},
{
"data": {
"text/plain": [
"('The radial distribution function (RDF) analysis for the simulation of the protein 1A3N solvated in water has been successfully completed. The RDF plot has been generated and is available for review.\\n\\nFinal Answer: The RDF analysis for the simulation of the protein 1A3N solvated in water has been successfully completed. The RDF plot has been generated and saved as `fig0_231508`. This plot provides insights into the spatial distribution of water molecules around the protein, which is crucial for understanding solvation effects and protein-water interactions.',\n",
" '5I7VMFV0')"
]
},
"execution_count": 3,
"metadata": {},
"output_type": "execute_result"
}
],
"source": [
Expand All @@ -217,9 +255,28 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 4,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"date and time: 2024-07-10\n",
"time: 23:15:13\n",
"Files found in registry: 1A3N_230454: PDB file downloaded from RSCB\n",
" PDBFile ID: 1A3N_230454\n",
" 1A3N_230519: 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_230525: Initial positions for simulation sim0_230525\n",
" sim0_230525: Basic Simulation of Protein 1A3N_230519\n",
" rec0_230532: Simulation trajectory for protein 1A3N_230519 and simulation sim0_230525\n",
" rec1_230532: Simulation state log for protein 1A3N_230519 and simulation sim0_230525\n",
" rec2_230532: Simulation pdb frames for protein 1A3N_230519 and simulation sim0_230525\n",
" fig0_231508: RDF plot for the trajectory file with id: rec0_230532\n"
]
}
],
"source": [
"now = datetime.datetime.now()\n",
"date = now.strftime(\"%Y-%m-%d\")\n",
Expand All @@ -233,26 +290,37 @@
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 6,
"metadata": {},
"outputs": [],
"source": [
"path_before = registry.get_mapped_path(\"1A3N_214800\")\n",
"path_after = registry.get_mapped_path(\"1A3N_214817\")\n",
"assert os.path.exists(path_before)\n",
"assert os.path.exists(path_after)\n",
"assert path_before != path_after"
"path_traj = registry.get_mapped_path(\"rec0_230532\")\n",
"path_top = registry.get_mapped_path(\"top_sim0_230525\")\n",
"assert os.path.exists(path_traj)\n",
"assert os.path.exists(path_top)\n",
"assert path_traj != path_top\n",
"\n",
"assert path_traj.endswith(\".dcd\")\n",
"assert path_top.endswith(\".pdb\")"
]
},
{
"cell_type": "code",
"execution_count": null,
"execution_count": 7,
"metadata": {},
"outputs": [],
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"Simulation with :24374 for 60 frames. Total time: 0.11800000000000001 ps\n"
]
}
],
"source": [
"import mdtraj as md\n",
"raw_file = md.load(path_before)\n",
"clean_file = md.load(path_after)"
"traj = md.load(path_traj, top=path_top)\n",
"print(f\"Simulation with :{traj.n_atoms} for {traj.n_frames} frames. Total time: {traj.time[-1]*0.002} ps\")"
]
},
{
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