Larsen2021-C2

Files for generating simulations in the paper:
Binding of Ca2+-Independent C2 Domains to Lipid Membranes: a Multi-Scale Molecular Dynamics Study Andreas Haahr Larsen and Mark S. P. Sansom

Published in Structure (open access):
https://doi.org/10.1016/j.str.2021.05.011

For questions/requests/collaborations, please contact Andreas Larsen: [email protected]

Overview of files:

Bash scripts

LOGBOOK_C2.sh: bash script to run coarse-grained simulations.
UMBRELLA.sh: bash script to run umbrella simulations and calculate PMFs.
LOGBOOK_FEP: bash script to run FEP calculations.
analysis.sh: bash script to analyze FEP calculations.
CG2AT.sh: bash script to convert from CG to AT with CG2AT.
LOGBOOK_AT.sh: bash script to run atomistic simulations.
LOGBOOK_analyze_AT: bash script to analyze atomistic simulations.

own python scripts

Dist_vs_time.py: calculates and plots Dist vs. time (Fig. 3).
Rzz_version2.py: calculates and plots Rzz vs dist (Fig. 4).
get_std_FEP.py: calculates std dev for FEP.
AT_analyze.py: analyze and plot for AT sims (Fig. 6).
Contacts.py: calculate PIP2 contacts (Fig. 7).
exponential_decay.py: fit exp docay to dist vs time (Fig. S1).
pmf_vs_contacts.py: plotting script for pmf vs contacts (Fig. S8).
extract_frames: extract frames for umbrella sampling, used in UMBRELLA.sh.
Dist_PIP2.py:
SHIP2_PMF_analyze:
Dist_vs_time_PTEN: calculate and plot dist vs time for larger-construct PTEN.

modified Martini scripts

martinize_GROMACS_2018_plumed.py: edited line 1851 to have "/gromacs/top/" instead of "/top/"

modified Martini topology files

martini_v2.0_lipids_all_201506.itp: added (optional) restaint on POP2, "POSRES_POP2"

plumed files

dist_ang_restraint_***.dat: Plumed files for each protein.

mdp files

note: some of the mdp files are copied and modified by LOGBOOK_C2.sh or UMBRELLA.sh or LOGBOOK_AT.sh before use.

minimization.mdp: CG minimization.
equilibration.mdp: CG equilibration.
production.mdp: CG production.
pull.mdp: CG umbrella preparation.
umbrella.mdp: CG umbrella run.
min.mdp: AT minimization.
nvt.mdp: AT NVT equilibration.
npt.mdp: AT NPT equilibration.
prod.mdp: AT production.
em_RFEP.mdp: FEP equilibration.
md_RFEP.mdp: FEP production.

pdb files (structures)

after modification by modeller.

***.pdb.

Other files

LOGBOOK_Folders: text file with overview of the content in the different folders (referred to in the bash scripts).
Overview.ods: overview of C2 structures (used for initial selection of structures).