Author: Leslie Salas-Estrada

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…

Lipid project

1. All-atom simulations of rhodopsin in SDPE bilayers
   • 100 ps-resolution trajectories and NAMD output files → hill:/scratch4tb/lsalas/all_atom/simulations
   • 1 ns trajectories
   • Analysis
2. All-atom simulations of neat SDPE bilayers
   • 100 ps-resolution trajectories and NAMD output files → hill:/scratch4tb/lsalas/all_atom/neatSDPE/extended
   • 1 ns trajectories
   • Analysis

SAXS project

1. All-atom simulations of rhodopsin in SDPE bilayers
   • Parent dark state trajectories → hill:/scratch4tb/lsalas/all_atom/simulations
   • 1 hv paired trajectories → hill:/run/media/lsalas/micelles_1hv/Work/micelles/1hv
   • Analysis
2. All-atom simulations of rhodopsin in CHAPS micelles
   • Parent dark state trajectories → hill:/scratch6tb/Work/saxs/micelles
   • 1 hv paired trajectories → hill:/run/media/lsalas/micelles_1hv/Work/micelles/1hv
   • Analysis → hill:/scratch6tb/Work/saxs/micelles/1hv and hill:/run/media/lsalas/micelles_1hv/Work/micelles/analysis
3. Water simulations
   • 240 Å box (458,957 waters, 1249 Na+, 1249 Cl-) → hill:/home/lsalas/Work/saxs/micelles/water/box_240A
   • 110 Å box (45,222 waters, 82 Na+, 82 Cl-) → hill:/home/lsalas/Work/saxs/micelles/water/box_110A

Go-models project

1. All-atom simulations of rhodopsin in SDPE bilayers
   • 100 ps trajectories and NAMD output files:
   • 1 ns trajectories:
   • 1 ns trajectories:
2. All-atom simulations of neat SDPE bilayers
   • 100 ps trajectories and NAMD output files:
   • 1 ns trajectories:
   • 1 ns trajectories:

Other projects

1. D-cysteine ethyl ester (DCEE)
   • 100 ps trajectories and NAMD output files:
   • 1 ns trajectories:
   • 1 ns trajectories:
2. Myoglobin
   • 100 ps trajectories and NAMD output files:
   • 1 ns trajectories:
   • 1 ns trajectories:
3. Alpha-synuclein
   • 100 ps trajectories and NAMD output files:
   • 1 ns trajectories:
   • 1 ns trajectories:
4. Fengycin
   • 100 ps trajectories and NAMD output files:
   • 1 ns trajectories:
   • 1 ns trajectories:

Git repository

Location → membrane:/domicile/git/repos/LabMembers/lsalas

1. Code → membrane:/domicile/git/repos/LabMembers/lsalas/code
   • lipids
   • saxs
   • multiwell
   • dcee
   • myoglobin
   • synuclein
   • fengycin
2. Papers
   • Lipids → membrane:/domicile/git/repos/LabMembers/lsalas/papers/lipids.git
   • SAXS → membrane:/domicile/git/repos/LabMembers/lsalas/papers/saxs.git
   • Thesis → membrane:/domicile/git/repos/LabMembers/lsalas/papers/thesis.git
   • Thesis template → membrane:/domicile/git/repos/LabMembers/lsalas/papers/thesis.git
3. Posters
   • BPS 2015: Retinal dynamics → membrane:/domicile/git/repos/LabMembers/lsalas/posters/bps2015.git
   • BPS 2016: Lipid project → membrane:/domicile/git/repos/LabMembers/lsalas/posters/bps2016.git
   • BPS 2017: Go-models → membrane:/domicile/git/repos/LabMembers/lsalas/posters/bps2017.git
   • BPS 2018: Go-models → membrane:/domicile/git/repos/LabMembers/lsalas/posters/bps2018.git
   • BPS 2019: SAXS bilayers → membrane:/domicile/git/repos/LabMembers/lsalas/posters/bps2019.git
   • BPS 2020: SAXS bilayers and micelles → membrane:/domicile/git/repos/LabMembers/lsalas/posters/bps2020.git
4. Presentations
   • Student seminar 2015: Retinal dynamics → membrane:/domicile/git/repos/LabMembers/lsalas/presentations/ss2015.git
   • Student seminar 2016: Lipid project → membrane:/domicile/git/repos/LabMembers/lsalas/presentations/ss2016.git
   • Student seminar 2017: Go-models → membrane:/domicile/git/repos/LabMembers/lsalas/presentations/ss2017.git
   • Student seminar 2018: SAXS and Go-models → membrane:/domicile/git/repos/LabMembers/lsalas/presentations/ss2018.git
   • Student seminar 2019: SAXS → membrane:/domicile/git/repos/LabMembers/lsalas/presentations/ss2019.git
   • Thesis defense 2019: Lipids and SAXS → membrane:/domicile/git/repos/LabMembers/lsalas/presentations/td2019.git

GitHub repository

Location: https://github.com/lsalases

1. bhcycler → https://github.com/lsalases/bhcycler

   Cycler to submit jobs iteratively on BlueHive (with OpenMM templates).

2. loos → https://github.com/lsalases/loos

   Fork of LOOS that contains branches for edits/additions to OMG, checking the chirality of a selection, and building a protein/micelle system.