molecular-dynamics

Molecular dynamics simulation models protein stability and conformational changes by calculating atomic interactions over time using OpenMM. It solves the problem of understanding dynamic biophysical behaviors that static structures cannot provide, facilitating research in structural biology and drug discovery.

To run molecular dynamics, prepare your system from a PDB file by applying solvation and force fields, then execute energy minimization, NVT, and NPT equilibration before production simulation. This skill uses OpenMM to automate the setup and execution of these molecular dynamics stages.

Analyze molecular dynamics trajectories for RMSD, RMSF, and contact maps using MDAnalysis for post-processing. This skill calculates these biophysical properties from the simulation output to help you evaluate protein stability and structural fluctuations.

Yes, you can investigate how a specific mutation affects target protein stability by running a molecular dynamics simulation with OpenMM and analyzing the resulting trajectory with MDAnalysis. This workflow models the conformational ensemble to reveal dynamic structural impacts.

The molecular dynamics simulation supports various force fields for system preparation and multiple trajectory formats for analysis. It leverages OpenMM for simulation execution and MDAnalysis for trajectory post-processing to ensure flexibility in biophysics research.