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Molecular dynamics simulation setup, execution, and trajectory analysis
Passed 17 of 22 test cases with the skill, and 14 of 22 without it.
and 4 more in the full report
3 fixed14 passed either way5 still failing0 broke
Tokens, turns and time describe resource use, not a dollar price.
One of 3 test cases the skill fixed. Same model, same prompt, with and without the skill.
Could you write a Python function using OpenMM that takes a PDB file path, temperature, pressure, and integration timestep, and builds a fully prepared simulation system? It should add solvent/ions, set up nonbonded settings and Langevin dynamics, attach a pressure control barostat, perform energy minimization, and return the configured Simulation instance.
| Checked | Without skill | With skill |
|---|---|---|
| Uses 'amber14/tip3pfb.xml' as the water force field XML file | Missed | Passed |
| Multiplies the pressure value by the atmospheres unit object when instantiating MonteCarloBarostat | Missed | Passed |
The instructions your model reads when the skill loads.
A skill for setting up, running, and analyzing molecular dynamics (MD) simulations. Covers force field selection, system preparation, simulation protocols, trajectory analysis, and free energy calculations using GROMACS, OpenMM, and MDAnalysis.
The standard workflow for preparing an MD simulation:
1. Obtain structure (PDB, homology model, or docking pose)
2. Clean structure (add missing atoms, fix protonation states)
3. Assign force field parameters
4. Solvate in explicit water box
5. Add counterions to neutralize charge
6. Energy minimize
7. Equilibrate (NVT then NPT)
8. Production run
# 1. Generate topology from PDB
gmx pdb2gmx -f protein.pdb -o processed.gro -water tip3p -ff amber99sb-ildn
# 2. Define simulation box (dodecahedron, 1.0 nm buffer)
gmx editconf -f processed.gro -o boxed.gro -c -d 1.0 -bt dodecahedron
# 3. Solvate
gmx solvate -cp boxed.gro -cs spc216.gro -o solvated.gro -p topol.top
# 4. Add ions to neutralize and set ionic strength (0.15 M NaCl)
gmx grompp -f ions.mdp -c solvated.gro -p topol.top -o ions.tpr
gmx genion -s ions.tpr -o ionized.gro -p topol.top -pname NA -nname CL -neutral -conc 0.15
# 5. Energy minimization
gmx grompp -f minim.mdp -c ionized.gro -p topol.top -o em.tpr
gmx mdrun -deffnm em
test cases passed, vs 14 / 22 without
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