Project ID: plumID:21.046
Name: Ubiquitin Interacting Motifs, Duality Between Structured and Disordered Motifs
Archive: https://github.com/ELELAB/disoUIM/raw/main/plumednest/plumednest.zip
Category: bio
Keywords: wt metadynamics, ubiquitin, ataxin-3, short linear motifs, ubiquitin binding motif, moonlight functions, intrinsic disorder
PLUMED version: 2.3
Contributor: Elena Papaleo
Submitted on: 11 Nov 2021
Publication: M. Lambrughi et al., Ubiquitin Interacting Motifs: Duality Between Structured and Disordered Motifs, Frontiers in Molecular Biosciences 8 (2021)

PLUMED input files

File Compatible with
WT-metaD.a032005/plumed2.dat tested on v2.8 tested on master
WT-metaD.a03ws/plumed2.dat tested on v2.8 tested on master
WT-metaD.c22star/plumed2.dat tested on v2.8 tested on master

Last tested: 30 Nov 2021, 15:06:19

Project description and instructions
Here we include the files to reproduce the WT-metaD simulations associated with the publication Lambrughi M, Maiani E, Aykac Fas B, Shaw GS, Kragelund BB, Lindorff-Larsen K, Teilum K, Invernizzi G and Papaleo E (2021) Ubiquitin Interacting Motifs. Duality Between Structured and Disordered Motifs. Front. Mol. Biosci. 8 676235. We include the files to reproduce the WT-metaD simulation with i) Amber ff03w force field with the TIP4P/2005 (folder WT-metaD.a032005), ii) Amber ff03ws with TIP4P/2005 water model with modified protein–water pair interactions, iii) CHARMM22star force field with TIPS3P water model. For each of the three metadynamics included in the publication, we provide the input files (plumed2.dat plumed.dat sim.tpr). The simulations were performed using GROMACS 4.6.2 and PLUMED 1.3. We converted plumed.dat in the formalism of PLUMED 2 in the plumed2.dat and tested it using GROMACS 5.1.2 and PLUMED 2.3.

Submission history
[v1] 11 Nov 2021: original submission

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plumeDnest:21.046