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Run and analyze molecular dynamics simulations with OpenMM and MDAnalysis. Set up protein/small molecule systems, define force fields, run energy minimization and production MD, analyze trajectories (RMSD, RMSF, contact maps, free energy surfaces). For structural biology, drug binding, and biophysics.
Passed 13 of 21 test cases with the skill, and 12 of 21 without it.
and 1 more in the full report
2 fixed12 passed either way7 still failing1 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 2 test cases the skill fixed. Same model, same prompt, with and without the skill.
I am setting up a classical molecular dynamics simulation for a standard globular protein like lysozyme in explicit solvent. Many tutorials recommend older force fields like AMBER99SB with standard TIP3P. What modern force field and water model pair should I select for standard proteins?
| Checked | Without skill | With skill |
|---|---|---|
| Specifies AMBER14 or amber14-all.xml as the force field. | Missed | Passed |
| Specifies TIP3P-FB as the explicit water model. | Missed | Passed |
The instructions your model reads when the skill loads.
--|------------------------|-------------|
| Standard proteins | AMBER14 (amber14-all.xml) | TIP3P-FB |
| Proteins + small molecules | AMBER14 + GAFF2 | TIP3P-FB |
| Membrane proteins | CHARMM36m | TIP3P |
| Nucleic acids | AMBER99-bsc1 or AMBER14 | TIP3P |
| Disordered proteins | ff19SB or CHARMM36m | TIP3P |
from pdbfixer import PDBFixer
from openmm.app import PDBFile
def fix_pdb(input_pdb, output_pdb, ph=7.0):
"""Fix common PDB issues: missing residues, atoms, add H, standardize."""
fixer = PDBFixer(filename=input_pdb)
fixer.findMissingResidues()
fixer.findNonstandardResidues()
fixer.replaceNonstandardResidues()
fixer.removeHeterogens(True) # Remove water/ligands
fixer.findMissingAtoms()
fixer.addMissingAtoms()
fixer.addMissingHydrogens(ph)
with open(output_pdb, 'w') as f:
PDBFile.writeFile(fixer.topology, fixer.positions, f)
return output_pdb
# For ligand parameterization, use OpenFF toolkit or ACPYPE
# pip install openff-toolkit
from openff.toolkit import Molecule, ForceField as OFFForceField
from openff.interchange import Interchange
test cases passed, vs 12 / 21 without
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