molecular-dynamics-guide
Molecular dynamics simulation setup, execution, and trajectory analysis
Profile →npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill molecular-dynamics-guide --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# Molecular Dynamics Guide 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. ## System Preparation ### Building a Simulation System 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 ``` ### GROMACS System Setup ```bash # 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.gr
- System Preparation
- Building a Simulation System
- GROMACS System Setup
- Force Field Selection
- Common Force Fields
- OpenMM System Setup
- Trajectory Analysis
- Structural Analysis with MDAnalysis
- Hydrogen Bond Analysis
- Free Energy Methods
- Umbrella Sampling
- Alchemical Free Energy Perturbation
- Tools and Software
gmx pdb2gmx -f protein.pdb -o processed.gro -water tip3p -ff amber99sb-ildn gmx editconf -f processed.gro -o boxed.gro -c -d 1.0 -bt dodecahedron gmx solvate -cp boxed.gro -cs spc216.gro -o solvated.gro -p topol.top 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 gmx grompp -f minim.mdp -c ionized.gro -p topol.top -o em.tpr gmx mdrun -deffnm em gmx grompp -f nvt.mdp -c em.gro -r em.gro -p topol.top -o nvt.tpr gmx mdrun -deffnm nvt gmx grompp -f npt.mdp -c nvt.gro -r nvt.gro -t nvt.cpt -p topol.top -o npt.tpr
What does the molecular-dynamics-guide skill do?
Molecular dynamics simulation setup, execution, and trajectory analysis
How do I install it?
Run `npx skills add brycewang-stanford/Auto-Empirical-Research-Skills --skill molecular-dynamics-guide --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From brycewang-stanford/Auto-Empirical-Research-Skills, a repository with 3,244 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.