This codebook.txt file was generated on 20190621 by Vaidyanathan Sethuraman Please send comments/queries or bug reports to vsethura@umn.edu ------------------- GENERAL INFORMATION ------------------- 1. Title of Dataset: Simulation data and analysis/simulation codes for "Influence of Charge Sequence on the Adsorption of Polyelectrolytes to Oppositely-Charged Polyelectrolyte Brushes" 2. Author Information Principal Investigator Contact Information Name: Kevin Dorfman Institution: University of Minnesota Twin Cities Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email: dorfman@umn.edu Associate or Co-investigator Contact Information Name: Michael McGovern Institution: University of Minnesota Twin Cities Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Associate or Co-investigator Contact Information Name: David C. Morse Institution: University of Minnesota Twin Cities Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email: morse012@umn.edu Associate or Co-investigator Contact Information Name: Vaidyanathan Sethuraman Institution: University of Minnesota Twin Cities Address: Department of Chemical Engineering and Materials Science, 421 Washington Ave SE, Minneapolis, Minnesota 55455 Email: vsethura@umn.edu 3. Information about funding sources that supported the collection of the data: University of Minnesota Materials Science Research and Engineering Center under Award No. DMR-1420013. -------------------------- SHARING/ACCESS INFORMATION -------------------------- 1. Licenses/restrictions placed on the data: CC0 1.0 Universal, http://creativecommons.org/publicdomain/zero/1.0/ 2. Links to publications that cite or use the data: Sethuraman, Vaidyanathan, Michael McGovern, David Morse, and Kevin Dorfman. "Influence of Charge Sequence on the Adsorption of Polyelectrolytes to Oppositely-Charged Polyelectrolyte Brushes." Soft matter (2019). https://doi.org/10.1039/C9SM00581A. 3. Links to other publicly accessible locations of the data: Codes for generating, running, and analysis: https://github.com/vaidyanathanms/polyelectrolyte_sequencedependence.git 4. Links/relationships to ancillary data sets: See (3) 5. Was data derived from another source? No If yes, list source(s): N/A 6. Citation for this dataset: Sethuraman, Vaidyanathan; McGovern, Michael; Morse, David C; Dorfman, Kevin D. (2019). Simulation data for "Influence of charge sequence on the adsorption of polyelectrolytes to oppositely-charged polyelectrolyte brushes". Retrieved from the Data Repository for the University of Minnesota, https://doi.org/10.13020/bytm-ae84. --------------------- DATA & FILE OVERVIEW --------------------- Software packages required: LAMMPS (Version - 11 Aug 2017) or later, FORTRAN 90/95, MATLAB 2017b or later, Python 3.0 or later, VMD 1.9.1. Compilers required: mkl, qopenmp, ifort LAMMPS should be compiled with kspace, molecule and USER-COLVARS package. 1. File List There are 148 directories, 1289 files in this dataset. See ./tree.dat to see the file structure. See also ./src/codes_usage/codes_usage.pdf for a detailed list of the files used 2. Relationship between files: FORTRAN files are used to generate initial configuration and to analyze trajectories. LAMMPS files are used to generate trajectories. Python files are used to do parameter sweeps. MATLAB files are used to post process analyzed files and to plot output data. In Section 8 of the codes_usage.pdf, a flow chart is provided as a guidance to generate and analyze trajectory files using the codes provided with this data set. ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fig 2 ----------------------------------------- Filename: adsorbed_chain_ave_rcut_1.50.dat -- This file contains the data that is given in Fig. 2 of the paper col1: (number of polyanions) col2: (Architecture: bl = block; al = alter) col3: (fraction adsorbed/number of brush) Filename: htcutoff_all.dat - Supplementary data for the height of the brush col1: (number of polyanions) col2: (Architecture: bl = block; al = alter) col3: (height units of sigma) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fig 3 ----------------------------------------- col1: (number of polyanions) col2: (Architecture: bl = block; al = alter) col3: (cut off used to compute free energy) col4: (free energy in kBT units) col5: (error in kBT units) ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fig 4 ----------------------------------------- Filename - AllEner.dat -- Data plotted in Figs (4a) and (4b) of the main manuscript col1: (number of polyanions) col2: (Architecture: bl = block; al = alter) col3: (Free energy in kBT units) col4: (Internal energy in kBT units) col5: (delta N between biased and unbiased) col6: (delU/delN in kbT units -- Fig 4a yaxis) col7: (entropy in kbT units -- Fig 4b yaxis) Filename - DeltaN_1.50.dat -- Supplementary data showing the difference in number of chains between biased and unbiased simulations Filename - AvgUnBiasEnergy_nbias.dat -- Supplementary data showing the average unbiased energy Filename - AvgBiasEnergy_nbias_5.dat -- Supplementary data showing the average biased energy ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fig 5 ----------------------------------------- Each folder is named results_72_xx_yy xx and yy can be bl(for block) or al(for alternating) architechtures Each of the cases correspond to those in Figs. 5a-d In each of the folder use the file dens.lammpstrj Each of these files will have 8 columns col1: dist from the surface col2: density of spacer block col3: density of neutral block of polycations col4: density of charged block of polycations col5: density of neutral block of polyanions col6: density of charged block of polyanions col7: density of positive ions col8: density of negative ions ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fig 6 ----------------------------------------- Each folder is named results_32_xx_yy (similar to Fig_5) xx and yy can be bl(for block) or al(for alternating) architechtures Each of the cases correspond to those in Figs. 6a-d In each of the folder use the file dens.lammpstrj Each of these files will have 8 columns col1: dist from the surface col2: density of spacer block col3: density of neutral block of polycations col4: density of charged block of polycations col5: density of neutral block of polyanions col6: density of charged block of polyanions col7: density of positive ions col8: density of negative ions ----------------------------------------- DATA-SPECIFIC INFORMATION FOR: Fig 7 ----------------------------------------- Fig. 7(a) Each folder is named results_100_xx_yy xx and yy can be bl(for block) or al(for alternating) architechtures In each of the folder use the file dens.lammpstrj Each of these files will have 8 columns col1: dist from the surface col2: density of spacer block (charge 0) col3: density of neutral block of polycations (charge 0) col4: density of charged block of polycations (charge +1) col5: density of neutral block of polyanions (charge 0) col6: density of charged block of polyanions (charge -1) col7: density of positive ions (charge +1) col8: density of negative ions (charge -1) Multiply each column by its corresponding charge to get the charge density. Fig. 7(b) In each file, the net charge within the brush region is given as a function of architechture of the block ---------------------------------------------- DATA-SPECIFIC INFORMATION FOR ALL DIRECTORIES ---------------------------------------------- all_txtfiles - MATLAB runs output their files here. Biascalc - contains all files from biased and unbiased calculations. err_data - contains error data for all figures. whamout_all - contains free energy data and WHAM data as a function of distance from the surface. results_adsfrac - contains the adsorbed chain/monomer fraction for each case. results_dens - contains the density profile for spacer/neutral/charged blocks of polycation, neutral/charged blocks of polyanion and counter ions for each case. fig_data - contains data specific information for each figure in the manuscript. src - contains source codes.