DOI: 10.5281/zenodo.5592299
title: Supplemental material for "Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation"

description: Input-scripts and data-files from the Cellulose article "Computational study of the dissolution of cellulose into single chains: the role of the solvent and agitation" by Bering, E., Torstensen, J., Lervik, A., Wijn, A. S. # Content The folder "glycamstructures" contains the output from GLYCAM carbohydrate builder with force-field parameters, coordinates and topology of a single chain of cellulose composed of 4 cellobiose units. The folder "intermol" contains the output from the software Intermol were the content of "glycamstructures" is translated into the lingo of LAMMPS. The folder "packmol" contains input files for the software Packmol, which was used for creating coordinate-files for solvated systems of cellulose with water and cellulose with the solvent mixture. (The bash-script clean.sh fixes the formatting of the .xyz-files such that LAMMPS can read it.) The folder "36bundle" contains input files for creating the initial configuration of the bundle with 36 chains in a maze configuration, namely 36bundle.sh reads 1chain.xyz to make the coordinate file 36bundle.xyz. Further, nvt00.in is the initial LAMMPS script for slowly starting up this system with the NVT-ensemble, which reads system information from the LAMMPS-datafile chain.36bundle, cellulose parameters from the LAMMPS-datafile data.cellulose_nohybrid and coordinates from 36bundle.xyz. nvt01.in and nvt02.in continues sequentially, resulting in the configuration stored in the LAMMPS data-file chain.nvt02. The folder "36bundle_mix" continues from 36bundle by first adding the solvent mixture with coordinates from Packmol in the file 36bm.xyz and slowly starting up in the NVT-ensemble with nvt00.in, with force-field parameters in data.cellulose.in, data.water_spce.in, data.naoh.in and data.urea.in, with charges and connectivity of the solvent molecules in the files water_spce.txt, naoh.txt and urea.txt. The LAMMPS script npt00.in continues with the NPT-ensemble, which is continued with npt01.in etc., resulting in the configuration stored in the LAMMPS data-file chain.npt06. These systems can be continued with length- or force-controlled oscillatory stretching/compression with osc_length.in and osc_force.in respectively, which was used to make the configurations stored in the LAMMPS data-files chain.osc_length4 and chain.osc_force4. Similarly, the folder "36bundle_water" continues from 36bundle by first adding the water with coordinates from Packmol in the file 36bw.xyz and slowly starting up in the NVT-ensemble with nvt00.in, with force-field parameters in data.cellulose.in and data.water_spce.in, with charges and connectivity of the water molecules in the file water_spce.txt. Again, these systems can be continued with length- or force-controlled oscillatory stretching/compression with osc_length.in and osc_force.in respectively, which was used to make the configurations stored in the LAMMPS data-files chain.osc_length4 and chain.osc_force4.
description: Funding provided by Research Council of Norway through project no. 250158 and project no. 262644. The simulations were performed on resources provided by UNINETT Sigma2 - the National Infrastructure for High Performance Computing and Data Storage in Norway and the Idun cluster provided by the NTNU High Performance Computing Group.