PLUMED-NEST

Project ID: plumID:26.009
Name: Exploring the Conformational Landscape of HIV-1 TAR RNA by PT-WTE
Archive: https://github.com/stefano-bosio/zip_for_nest/raw/main/tar-ensemble-modeling.zip
Category: bio
Keywords: RNA, PT-WTE, HIV-1 TAR
PLUMED version: 2.9
Contributor: Stefano Bosio
Submitted on: 14 Jul 2026
Publication: unpublished

PLUMED input files

File	Compatible with
repl_00/plumed.dat
repl_01/plumed.dat
repl_02/plumed.dat
repl_03/plumed.dat
repl_04/plumed.dat
repl_05/plumed.dat
repl_06/plumed.dat
repl_07/plumed.dat
repl_08/plumed.dat
repl_09/plumed.dat
repl_10/plumed.dat
repl_11/plumed.dat
repl_12/plumed.dat
repl_13/plumed.dat
repl_14/plumed.dat
repl_15/plumed.dat
repl_16/plumed.dat
repl_17/plumed.dat
repl_18/plumed.dat
repl_19/plumed.dat

Last tested: 14 Jul 2026, 14:05:01

Project description and instructions
Input files to perform PT-WTE molecular dynamics simulations of HIV-1 TAR RNA. Simulations were carried out using GROMACS 2023.2 patched with PLUMED 2.9. The Jupyter notebooks used for data analysis and figure generation are available here.

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

Submission history
[v1] 14 Jul 2026: original submission

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