Posted on by Leslie Salas-Estrada

Working Directories

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.