Collective Molecular Dynamics (CoMD) Simulations

Learn global transition pathways with multiscale hybrid methodology, collective molecular dynamics.

You can also read this tutorial in PDF format.

Plug-in files: ZIP TGZ

Tutorial files: ZIP TGZ

• Introduction
  • Installation
  • coMD Plugin
  • Tutorial Files
  • How to Cite
• Background
• Methodology
• Simulation Setup
  • Input Files
  • Protein Structures
  • Ionization Parameters
  • Minimization Parameters
  • Conformational Sampling with ANM Modes
  • Targeted Molecular Dynamics Parameters
  • Simulation Options
  • Output Options
  • Output Files
  • Simulation
• Collective Molecular Dynamics Analysis
  • Preparing Trajectory Files
  • Concatenating Trajectory Files
  • Principal Component Analysis
  • Visualization of Trajectories
• License

Acknowledgments

Continued development of Protein Dynamics Software ProDy and associated programs is partially supported by the NIH-funded R01 GM139297 entitled “Toward a deeper understanding of allostery and allotargeting by computational approaches”.