Data for: Synthetic Flagella Spin and Contract at the Expense of Chemical Fuel

Due to limitations on file size for this dataset, trajectory files are provided in the GROMACS
(.xtc) format, with the omission of water molecules (hence _dry.*) and for the last 5 ns of the 25 ns simulations. It is this portion of the simulation which was measured for the results described in the article.

Contents:

> ForceField.zip: contains the NAMD compatible martini-par and martini-top files alongside the NAMD
CpHMD executable *tcl file.

> Fmoc: contains the *top files for FmocAVD/FmocAAD/FmocVVD as well as for the Fmoc group.

> Reference: contains all files and results for alchemical fitting of delta-G values for the
anhydride group and its state switching between doubly and singly charged termini.

> Bilayer_grid_{2-4}: contain triplicate results for simulation of FmocAVD at various fuel levels
(e.g., from pH 1 - 4) which capture 100 - 0 % anhydride functionalisation. It is important to note
that the 'pH' set in a given dir is not reflective of the 'number' of the directory (e.g., FL5 = 3.40
and FL6 = 3.80). This convention was maintained for consistency with earlier results.

> pulled_{dirname}_{property}.csv -- contain measurements reported in the article.

~~~~ subdir ~~~~
> cphmd_dry.{xtc/gro} -- the dry, 5 ns trajectory of the bilayer at the end of the 25 ns eq.
> cphmd_out2.{psf/pdb} -- use these to visualise the structure at the end of the simulation.
> CPHLOG file details the charge state of each termini with the following meaning:

0 0 = doubly deprotonated
0 1 = singly deprotonated
1 0 = singly deprotonated
1 1 = anhydride functionality

> CPHMD2.inp -- this is the run parameter file
> CPHMD2.out -- this is the run output file.
> The executable is as follows, note the specially compiled version of NAMD_2.14 (included in this dataset)

/users/fjb15167/Constant_pH/NAMD_2.14_Source/Linux-x86_64-g++/namd2 +p$SLURM_NTASKS CPHMD2.inp > CPHMD2.out

> Bilayer_grid_structure_equilibrate: this file contains the equilibration of the starting structure for the simulation
of Bilayer_grid_{2-4} using straight MD (no CPHMD) and it is the coords/vels/xsc data pertained in these which are used
as inputs for the CPHMD simulations.

> Fmoc{AVD/AAD/VVD}_grid_{n}: these directories contain the run files for the different tripeptide
types at fuel levels FL1, FL3, FL7, FL8 and FL9.

> Fmoc{AVD/AAD/VVD}__structure_equilibrate: building and equilibration of system starting structures using 100 %
anhydride and no CPHMD method applied (e.g., straight MD equilibration).

> Scripts: this dir contains all relevant python scripts for the analysis of these systems

states_neighbours_master_3.0.py parses to identify the population of the anhydride/non-anhydride (execute first).

analysis_master_3.0.py performs analysis of RDFs, dihedral stacking, SASA, length etc.

fresh_analysis.py is then used to nicely organise all output data into menagable formats for collaborators. These
are saved as pulled_{dirname}_{property}.csv.

> NAMD_2.14_Source: this contains the specially compiled version of NAMD which is required to run CPHMD simulations and this
must be made accessible in the *inp file for this mode of simulation.