Project ID: plumID:24.028
Name: All-atom simulations of RNA-membrane interactions
Archive: https://github.com/salvatoredimarco/rna-membrane/archive/main.zip (browse)
Category: bio
Keywords: metadynamics, membrane, RNA
PLUMED version: 2.9
Contributor: Giovanni Bussi
Submitted on: 07 Nov 2024
Last revised: 23 Apr 2025
Publication: S. Di Marco, J. Aupič, G. Bussi, A. Magistrato, All-Atom Simulations Elucidate the Molecular Mechanism Underlying RNA–Membrane Interactions. Nano Letters. 25, 4628–4635 (2025)

PLUMED input files

File Compatible with
inputs/opc/U/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/opc/G/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/opc/A/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/opc/C/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/16mer_elong/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/GGC/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/GA/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/A3/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/A2/metadyn/plumed_puckering.dat tested on v2.10 tested on master
inputs/tip3p/A2/metadyn/plumed_orientation.dat tested on v2.10 tested on master
inputs/tip3p/A2/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/GU/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/quadruplex/metadyn/plumed_pucker.dat tested on v2.10 tested on master
inputs/tip3p/quadruplex/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/CU/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/16mer_loose1/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/U/metadyn/plumed_puckering.dat tested on v2.10 tested on master
inputs/tip3p/U/metadyn/plumed_orientation.dat tested on v2.10 tested on master
inputs/tip3p/U/metadyn/plumed_metad.dat tested on v2.10 tested on master
inputs/tip3p/G/metadyn/plumed_puckering.dat tested on v2.10 tested on master

Last tested: 23 Apr 2025, 10:10:18

Project description and instructions
Scripts and inputs related to the preprint All-atom simulations elucidate the molecular mechanism underlying RNA-membrane interactions.

Submission history
[v1] 07 Nov 2024: original submission
[v2] 18 Mar 2025: fixed list of input files to reflect update in upstream repository
[v3] 23 Apr 2025: updated doi

Badge
Click on the image below and get the code to add the badge to your website!
plumeDnest:24.028