Eleftherios 'Lefteris' Mainas

Eleftherios 'Lefteris' Mainas

statistical mechanics + molecular simulations + quantum chemistry

Sunday Recap

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Research

The past week has been all about automation of the QM/MM1 workflow. QM/MM calculations are particurly tedious because of the extensive preparation of the system, meaning that there is a lot of case-by-case work and limited room for automation. My focus is on biliverdin2

  1. Perform long conventional Molecular Dynamics using a classical force field.
  2. Place biliverdin at the center of the box because it might have drifted away.
  3. Chop the long trajectory in N-equally spaced frames.
  4. Define a quantum mechanical region. In this case it is just biliverdin.
  5. Run QM/MM on each frame.

I automated steps 2-4 with a combination of AMBER’s cpptraj, pytraj and parmed programs. I need to figure out how to parse variables in the cpptraj program so that I can feed it N as the number of frames. Maybe will get back to it in the future…

Reading

I have been reading a lot about protein-protein dissociation. It is a rather complicated topic and requires rigorous study of the available computational methods in the literature.

Writing

I wrote a Methods section in my first post-doc paper and added the last paragraph/section in my PhD paper, that will soon be submitted.

  1. QM/MM (Quantum Mechanics/Molecular Mechanics): We treat the interesting part of the system with a quantum mechanical method like DFT and the rest of the system with a classical force field. Usually I like TeraChem for the quantum calculations and AMBER for the classical stuff. ↩

  2. Biliverdin: Tetrapyrrolic molecule that is a result of the breakdown of heme. This molecule can be found literally EVERYWHERE and it is a very common chromophore in fluorescent complexes. ↩