Project ID: plumID:21.015
Name: Coarse-grained metadynamics and umbrella sampling simulations to investigate interactions of carbohydrate-binding modules with chitin
Archive: https://github.com/gcourtade/papers/raw/master/2021/CBM5-CBM73-MetaD-US/CBM5-CBM73-MetaD-US.zip
Category: bio
Keywords: metadynamics, umbrella sampling, coarse-grained, MARTINI, chitin, carbohydrate-binding module
PLUMED version: 2.5
Contributor: Gaston Courtade
Submitted on: 15 Apr 2021
Last revised: 04 Aug 2021
Publication: E. Madland, Z. Forsberg, Y. Wang, K. Lindorff-Larsen, A. Niebisch, J. Modregger, V. G. H. Eijsink, F. L. Aachmann, G. Courtade, Structural and functional variation of chitin-binding domains of a lytic polysaccharide monooxygenase from Cellvibrio japonicus. Journal of Biological Chemistry. 297, 101084 (2021)
PLUMED input files
Last tested: 11 Sep 2024, 14:36:25
Project description and instructions
To run MetaD on CBM5, please use MetaD/CBM5/run_gmx.sh and the postprocessing script MetaD/CBM5/post_processing/Flow_post-processing.sh. To run MetaD on CBM73, please use MetaD/CBM73/run_gmx.sh and the postprocessing script MetaD/CBM73/post_processing/Flow_post-processing.sh. To run Umbrella Sampling simulations, please use US/CBM5/submit{0-22}.sh and US/CBM73/submit{0-22}.sh. All simulations have been performed with PLUMED v2.5 and GROMACS 5.1.4.
Submission history
[v1] 15 Apr 2021: original submission
[v2] 04 Aug 2021: updated doi
Badge
Click on the image below and get the code to add the badge to your website!
