09 February 2025 0 682 Report

Thank you for taking the time to read my question.

I am interested in computational approaches to studying the binding affinity between proteins and metal ions. Methods such as Molecular Dynamics (MD) simulations and Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid techniques seem to be useful for this purpose. However, I am not entirely sure how to set up and execute such calculations effectively.

If anyone has experience in this area, I would be truly grateful if you could share specific scripts or workflows using software such as GROMACS, NAMD, or any other relevant tools. A script that includes the necessary commands would be particularly helpful, as it would allow me to study both the computational implementation and the underlying theoretical principles simultaneously.

Additionally, if there are any recommended tutorials or resources for learning these techniques, I would sincerely appreciate your guidance. My goal is to learn by reviewing and running the code while deepening my understanding of the theoretical foundations.

Thank you in advance for your time and support. I truly appreciate any insights you may have.

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