Project ID: plumID:22.035
Name: Deciphering the alphabet of disorder — Glu and Asp act differently on local but not global properties
Archive: https://github.com/KULL-Centre/_2022_Roesgaard-Lundsgaard_DSS1/raw/main/plumed-input.zip
Category: bio
Keywords: intrinsically disordered proteins, parallel bias metadynamics, protein
PLUMED version: 2.6.1
Contributor: Kresten Lindorff-Larsen
Submitted on: 24 Sep 2022
Publication: M. A. Roesgaard, J. E. Lundsgaard, E. A. Newcombe, N. L. Jacobsen, F. Pesce, E. E. Tranchant, S. Lindemose, A. Prestel, R. Hartmann-Petersen, K. Lindorff-Larsen, B. B. Kragelund, Deciphering the Alphabet of Disorder—Glu and Asp Act Differently on Local but Not Global Properties. Biomolecules. 12, 1426 (2022)

PLUMED input files

File Compatible with
allD.dat tested on v2.9 tested on master
allD_helix.dat tested on v2.9 tested on master
allE.dat tested on v2.9 tested on master
allE_helix.dat tested on v2.9 tested on master
swap.dat tested on v2.9 tested on master
swap_helix.dat tested on v2.9 tested on master
wt.dat tested on v2.9 tested on master
wt_helix.dat tested on v2.9 tested on master

Last tested: 23 May 2024, 16:10:02

Project description and instructions
Software used. GROMACS v. 2019.6, cuda toolkit 10.2.89, openmpi 1.10.2. Example command line. mpirun -np 160 ${gmx} mdrun -deffnm wt_helix_prod -plumed wt_helix.dat -pin on -npme 0 -notunepme -v -maxh 0.5 -cpi -cpt 360.

Submission history
[v1] 24 Sep 2022: original submission

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:22.035