CG CELLULOSE FIBRIL

Creates coarse grain model of cellulose fibrils using MARTINI3 beads.

Author

Copyright (C) 2021-2022 Rodrigo Azevedo Moreira da Silva

IPPT-PAN Instytut Podstawowych Problemów Techniki Polskiej Akademii Nauk

Reference

The original paper describing the methodology

Moreira RA, Weber SAL, Poma AB. Martini 3 Model of Cellulose Microfibrils: On the Route to Capture Large Conformational Changes of Polysaccharides. Molecules. 2022; 27(3):976.

Usage

• Create a new folder with files of this repository.
• Download cellulose fibril from http://cces-sw.iqm.unicamp.br/cces/admin/cellulose/view;jsessionid= and copy the 'crystal.pdb' to the previously folder.
• Convert 'crystal.pdb' to gromacs format:

gmx editconf -f crystal.pdb -o fibril.gro

• Create the coarse grain model:

lua cgcellulose4PT2.lua

• Solvate the system:

gmx editconf -f cg-coordinates.gro -o cg-coordinates-newbox.gro -c -d 2.5 -bt triclinic
gmx solvate -radius 0.21 -cp cg-coordinates-newbox.gro -cs water-box-CG_303K-1bar.gro -o cg-coordinates-solvated.gro -p topol.top

Should proceed with minimization, NVT, NPT and MD runs.

Some examples of GROMACS .mdp files are included.

• Always double-check the input/output files!
• We recommend to coarse-grain configuration from a previously all-atom simulation run.
• The model is been developed, all contributions are welcome!

License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0).

Enjoy!