Project ID: plumID:21.017
Name: All-atom simulations of the Vav1 AD construct
Archive: https://zenodo.org/record/4733551/files/plumed.zip
Category: bio
Keywords: metadynamics, parallel-bias, well-tempered
PLUMED version: 2.5
Contributor: Simone Orioli
Submitted on: 27 Apr 2021
Last revised: 09 Dec 2021
Publication: S. Orioli, C. G. Henning Hansen, K. Lindorff-Larsen, Transient exposure of a buried phosphorylation site in an autoinhibited protein. Biophysical Journal. 121, 91–101 (2022)

PLUMED input files

File Compatible with
plumed/pbmetad/plumed.dat tested on v2.10 tested on master
plumed/pbmetad/reweight.dat tested on v2.10 tested on master
plumed/md/nmr_disp.dat tested on v2.10 tested on master
plumed/md/nmr_c36m.dat tested on v2.10 tested on master
plumed/md/cry_disp.dat tested on v2.10 tested on master
plumed/md/cry_c36m.dat tested on v2.10 tested on master
plumed/md/shootings.dat tested on v2.10 tested on master
plumed/wtmetad/plumed.dat tested on v2.10 tested on master
plumed/wtmetad/reweight.dat tested on v2.10 tested on master

Last tested: 06 Feb 2025, 16:12:31

Project description and instructions
The scripts are needed to reproduce and reweight the metadynamics simulations (WTMetaD and PBMetaD) and to calculate the CVs from the all-atom MD simulations. Simulations have been performed with Gromacs 2018.6 and Plumed 2.5.0

Submission history
[v1] 27 Apr 2021: original submission
[v2] 04 Aug 2021: updated doi
[v3] 09 Dec 2021: updated doi

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plumeDnest:21.017