MD simulation of amyloid beta dimer using GROMACS

[pchapain]

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

 

[NateD]

Hi Pinto, Thanks for your question. You can use the GROMACS tools to simulate a dimer of amyloid beta peptide in a water box. The first step is to prepare the necessary files. You can use the pdb file (1IYT) as a starting point. To create the input files, you need to edit the pdb file to add the extra peptide and also create a topology file. This can be done using the 'pdb2gmx' command. Once you have the necessary files, you can set up the simulation box. You can use the 'editconf' command to create a cuboidal box of appropriate size, centered on the peptides, with the desired amount of solvent. Then use the 'genbox' command to add the solvent molecules to the simulation box.Next you need to minimize the energy of the system. This can be done using the 'grompp' and 'mdrun' commands. After the energy minimization, you can run MD simulations to observe any dimer or β-sheet formation. For more information on using GROMACS for simulations, you can refer to the official manual or online tutorials.Hope this helps. Regards, GROMACS Expert