MD simulation of amyloid beta dimer using GROMACS

  • Thread starter pchapain
  • Start date
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
 

Want to reply to this thread?

"MD simulation of amyloid beta dimer using GROMACS" You must log in or register to reply here.

Physics Forums Values

We Value Quality
• Topics based on mainstream science
• Proper English grammar and spelling
We Value Civility
• Positive and compassionate attitudes
• Patience while debating
We Value Productivity
• Disciplined to remain on-topic
• Recognition of own weaknesses
• Solo and co-op problem solving
Top