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I am looking to outsource a set of comparative Molecular Dynamics (MD) simulations to evaluate whether Sulindac binding can stabilize the Alzheimer’s-associated R47H TREM2 mutant. Could you please perform the following? MD Systems to Prepare Please prepare and simulate three systems: Wild-type TREM2 (apo) R47H TREM2 (apo) R47H TREM2 + Sulindac (docked pose will be provided) Simulation Requirements Force field: CHARMM36 or AMBER99SB-ILDN Water model: TIP3P Add neutralizing ions (Na⁺/Cl⁻) Perform energy minimization, NVT, and NPT equilibration Run ~50 ns production MD (minimum 20 ns acceptable) Analyses Needed Please generate the following comparative metrics for all three systems: RMSD vs time RMSF per residue (focus around residue 47) Radius of gyration (Rg) Hydrogen-bond analysis (intra-protein + protein–ligand) SASA Secondary structure analysis (DSSP) These metrics are essential to evaluate whether Sulindac produces measurable structural stabilization of the R47H variant. Final Deliverables RMSD, RMSF, Rg, H-bond, SASA, and DSSP plots Final structures (.pdb) Trajectory files (.xtc) Simulation logs A brief comparison summary (5–6 lines) for: WT vs R47H R47H apo vs R47H + Sulindac Project Goal These simulations will directly test my hypothesis that Sulindac binding may stabilize the structurally weakened R47H TREM2 mutant. Thank you, Roy