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

File Compatible with
MetaD/CBM5/post_processing/coordination-groups.dat tested on v2.9 tested on master
MetaD/CBM5/post_processing/calc-weights.dat tested on v2.9 tested on master
MetaD/CBM5/plumed.dat tested on v2.9 tested on master
…etaD/CBM73/post_processing/coordination-groups.dat tested on v2.9 tested on master
…D/CBM73/post_processing/plumed_post_processing.dat tested on v2.9 tested on master
MetaD/CBM73/plumed.dat tested on v2.9 tested on master
US/CBM5/plumed12.dat tested on v2.9 tested on master
US/CBM5/plumed13.dat tested on v2.9 tested on master
US/CBM5/plumed11.dat tested on v2.9 tested on master
US/CBM5/plumed10.dat tested on v2.9 tested on master
US/CBM5/plumed14.dat tested on v2.9 tested on master
US/CBM5/plumed15.dat tested on v2.9 tested on master
US/CBM5/plumed17.dat tested on v2.9 tested on master
US/CBM5/plumed8.dat tested on v2.9 tested on master
US/CBM5/plumed9.dat tested on v2.9 tested on master
US/CBM5/plumed16.dat tested on v2.9 tested on master
US/CBM5/plumed4.dat tested on v2.9 tested on master
US/CBM5/plumed5.dat tested on v2.9 tested on master
US/CBM5/plumed18.dat tested on v2.9 tested on master
US/CBM5/plumed7.dat tested on v2.9 tested on master

Last tested: 27 Mar 2024, 17:01:11

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

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plumeDnest:21.015