Project ID: plumID:26.006
Name: Metadynamics simulations of buried phosphorylation sites and proline isomerisation
Archive: https://github.com/julian-streit/PTM_MD_analyses/raw/main/PLUMED.zip
Category: bio
Keywords: metadynamics
PLUMED version: 2.9
Contributor: Julian Streit
Submitted on: 12 May 2026
Publication: B. Lang, J. O. Streit, R. W. Kriwacki, J. Christodoulou, M. M. Babu, Protein Dynamics at Different Timescales Unlock Access to Hidden Post-Translational Modification Sites. doi: 10.1101/2025.06.25.661537 (2025)

PLUMED input files

File Compatible with
FLN5_FL_METAD/plumed.dat tested on v2.10 tested on master
FLN5_U_METAD/plumed.dat tested on v2.10 tested on master
FLNA21_METAD/plumed.dat tested on v2.10 tested on master
FLNA21_pS2319_trans_METAD/plumed.dat tested on v2.10 tested on master
FLNC24_METAD/plumed.dat tested on v2.10 tested on master
FLNC24_pS2718_trans_METAD/plumed.dat tested on v2.10 tested on master
PARK7_METAD_chainA/plumed.dat tested on v2.10 tested on master
PARK7_TYR_COORD_METAD_BF40/plumed.dat tested on v2.10 tested on master
PARK7_chainA_pY67_TYR_COORD_METAD_BF40/plumed.dat tested on v2.10 tested on master

Last tested: 19 May 2026, 16:35:43

Project description and instructions
plumed.dat activates the METAD bias for a new simulation. Simulations were performed with GROMACS 2022.4 + GROMACS 2.8.2 (FLN5) and GROMACS 2020.4 + PLUMED 2.6.2 or GROMACS 2023.5 + PLUMED 2.9.3 for FLNA21, FLNC24, PARK7.

Click here to open manual pages for actions used in this project.

Submission history
[v1] 12 May 2026: original submission

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plumeDnest:26.006