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
Publication: unpublished

PLUMED input files

File Compatible with
MetaD/CBM5/post_processing/coordination-groups.dat tested on v2.7 tested on master
MetaD/CBM5/post_processing/calc-weights.dat tested on v2.7 tested on master
MetaD/CBM5/plumed.dat tested on v2.7 tested on master
…etaD/CBM73/post_processing/coordination-groups.dat tested on v2.7 tested on master
…D/CBM73/post_processing/plumed_post_processing.dat tested on v2.7 tested on master
MetaD/CBM73/plumed.dat tested on v2.7 tested on master
US/CBM5/plumed12.dat tested on v2.7 tested on master
US/CBM5/plumed13.dat tested on v2.7 tested on master
US/CBM5/plumed11.dat tested on v2.7 tested on master
US/CBM5/plumed10.dat tested on v2.7 tested on master
US/CBM5/plumed14.dat tested on v2.7 tested on master
US/CBM5/plumed15.dat tested on v2.7 tested on master
US/CBM5/plumed17.dat tested on v2.7 tested on master
US/CBM5/plumed8.dat tested on v2.7 tested on master
US/CBM5/plumed9.dat tested on v2.7 tested on master
US/CBM5/plumed16.dat tested on v2.7 tested on master
US/CBM5/plumed4.dat tested on v2.7 tested on master
US/CBM5/plumed5.dat tested on v2.7 tested on master
US/CBM5/plumed18.dat tested on v2.7 tested on master
US/CBM5/plumed7.dat tested on v2.7 tested on master
US/CBM5/plumed6.dat tested on v2.7 tested on master
US/CBM5/plumed19.dat tested on v2.7 tested on master
US/CBM5/plumed21.dat tested on v2.7 tested on master
US/CBM5/plumed2.dat tested on v2.7 tested on master
US/CBM5/plumed3.dat tested on v2.7 tested on master
US/CBM5/plumed20.dat tested on v2.7 tested on master
US/CBM5/plumed22.dat tested on v2.7 tested on master
US/CBM5/plumed1.dat tested on v2.7 tested on master
US/CBM5/plumed0.dat tested on v2.7 tested on master
US/CBM73/plumed12.dat tested on v2.7 tested on master
US/CBM73/plumed13.dat tested on v2.7 tested on master
US/CBM73/plumed11.dat tested on v2.7 tested on master
US/CBM73/plumed10.dat tested on v2.7 tested on master
US/CBM73/plumed14.dat tested on v2.7 tested on master
US/CBM73/plumed15.dat tested on v2.7 tested on master
US/CBM73/plumed17.dat tested on v2.7 tested on master
US/CBM73/plumed8.dat tested on v2.7 tested on master
US/CBM73/plumed9.dat tested on v2.7 tested on master
US/CBM73/plumed16.dat tested on v2.7 tested on master
US/CBM73/plumed4.dat tested on v2.7 tested on master
US/CBM73/plumed5.dat tested on v2.7 tested on master
US/CBM73/plumed18.dat tested on v2.7 tested on master
US/CBM73/plumed7.dat tested on v2.7 tested on master
US/CBM73/plumed6.dat tested on v2.7 tested on master
US/CBM73/plumed19.dat tested on v2.7 tested on master
US/CBM73/plumed21.dat tested on v2.7 tested on master
US/CBM73/plumed2.dat tested on v2.7 tested on master
US/CBM73/plumed3.dat tested on v2.7 tested on master
US/CBM73/plumed20.dat tested on v2.7 tested on master
US/CBM73/plumed22.dat tested on v2.7 tested on master
US/CBM73/plumed1.dat tested on v2.7 tested on master
US/CBM73/plumed0.dat tested on v2.7 tested on master

Last tested: 22 Jul 2021, 08:52:24

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

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