Peptide Synthesis

  1. tetrazole-peptide conjugate synthesis

Super Computation Clusters

  1. Get a hyak account.
  2. (Optional) Change the squeue format on hyak.
  3. Install ruby on hyak for MOPAC tasks.
  4. Download scripts for the following computations.
  5. Install Miniconda or other versions of Python.

MOPAC Tutorials

  1. PM6 geometry optimization.
  2. Born Oppenheimer Molecular Dynamics (BOMD).
  3. Sort and select geometries from the BOMD trajectory.
  4. Measure interatomic distances from BOMD trajectories.

Gaussian Tutorials

  1. Create and submit Gaussian tasks.
  2. Process optimization output.
  3. Process frequency and compute Gibbs Energy.
  4. Process tddft and plot absorption spectrum.
  5. Create and process NewtonX task.
  6. Compute mp2/ccsd energy.

Other Tutorials

  1. Calculate ion mobility in Helium and Nitrogen.
  2. Densum.