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MD simulation of amyloid beta dimer using GROMACS

  1. May 8, 2012 #1
    Hello,

    I am very new to GROMACS and needed some help with simple MD simulations. I have amyloid beta peptide (pdb code 1IYT) monomer that I need to place side by side in a water box, energy minimize and run the simulation. I have problems putting them together and creating the new necessary files for the simulation. I can work it out for a single peptide in a solvated system but can't figure out how to run the simulations for both together to see any β-sheet/dimer formation.
    Please help and be as detailed as possible as I am very new to GROMACS.

    Thanks,
    Pinto
     
  2. jcsd
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