I am performing molecular dynamics (MD) simulations on a complex system composed of a protein antigen and the Fv fragment of a monoclonal antibody using GROMACS 2024.3, and I have been running into persistent errors throughout the simulation workflow. I suspect the root cause of these issues is improper configuration of the mdp (molecular dynamics parameter) files for each step of the simulation pipeline. Therefore, I would like to ask for your help with the following two questions: 1. Would any community members who have worked on antigen-antibody complex systems be willing to share the complete set of mdp files for all core simulation steps (including energy minimization, NVT equilibration, NPT equilibration, and production MD)? 2. Are there any official mdp templates or parameter recommendations for this type of protein-protein (antigen-antibody) complex system that I may have overlooked? Thank you so much for your time, guidance and assistance!
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