Molecular Dynamics simulations COMMON MISTAKES

 

Once, I thought Molecular Dynamics simulations were simple:

Run the simulation → generate RMSD plot → write paper.

Then one day, I realized something uncomfortable…

A simulation can look “perfect” and still be completely wrong.

I’ve seen:
❌ proteins explode because of bad protonation
❌ beautiful trajectories with incorrect force fields
❌ “stable complexes” that were just equilibration artifacts

That’s when I understood:

MD is not about making movies of atoms.
It’s about extracting physically meaningful insights.

After working with cryo-EM structures, oligomeric assemblies, docking, PCA/FEL analysis, and long-timescale simulations, I started noticing the same mistakes appearing again and again across beginner and sometimes even published MD studies.

So I created this infographic:

🔥 Top 10 Common Mistakes in MD Simulations
(+ practical solutions for each)

Whether you use GROMACS, Desmond, AMBER, NAMD, or OpenMM, these pitfalls are incredibly common in:
• protein simulations
• ligand binding studies
• membrane systems
• cryo-EM refinement workflows
• MM/PBSA projects

If you work in:
🧬 Structural Biology
💊 Drug Discovery
🖥 Computational Biophysics
🔬 Cryo-EM
📊 Bioinformatics

…this may save you weeks or even months of wrong interpretation.

Which mistake do you think is the MOST common in published MD papers?

Mine would be:
👉 Overinterpreting RMSD and PCA without validating the biology.