Nick Leioatt’s Project List

Ongoing Projects

I guess this is just the all-atom ensemble stuff.

Old/Finished Projects

  • SMOG simulations and data → mcgee:/scratch/nleioatts/SMOG
  • ENM data → mcgee:/scratch/nleioatts/old-ENM-data
  • Michael retinal paper: ha! good luck… paper is a word document, so no version control. The plots/data are mostly stored in the following places:
    • Results pertaining to the simulations (no NMR comparison data):
      • Dark state → mcgee:/home/nleioatts/work/simulation/meta-i-rhod
      • Complex counterion → mcgee:/home/nleioatts/work/simulation/light-rhod
    • NMR data:
      • Raw NMR data and full histograms → mcgee:/home/nleioatts/work/nleioatts/Papers/Meta-I-NMR
    • Lineshape:
      • The lineshape fitting tools are in the sun, but should you run into problems check this directory → mcgee:/home/nleioatts/work/nleioatts/lineshape

Uncompleted Projects

CG rhodopsin in SDPE bilayer for Harel Weinstein. It might take more time to find out what progress I made than to regenerate the data… but just in case I have stored it.
  • Ran 8 trajectories of inactive rhodopsin using MARTINI FF → mcgee:/scratch/nleioatts/cg_simulations/inactive
  • TODO:
    • Run counterpart simulations of active state. This was started, but I ran into problems with GROMACS and ran out of time to debug them… unfortunately there isn’t much here but see → mcgee:/home/nleioatts/work/cg_simulation/act
    • For some info, probably best to start over for active sims though…