Description
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.
(.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.
Date made available | 29 Aug 2024 |
---|---|
Publisher | University of Strathclyde |