[gmx-developers] Dimer Simulation Help

[Prakash Chapain]

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.
I found an exact similar situation as mine on a thread which is listed
below, but even following the thread did not provide the needed help:
http://lists.gromacs.org/pipermail/gmx-users/2007-September/029541.html

Thanks, Prakash.
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