Project ID: plumID:22.013
Name: Ligand dissociation from PreQ1 riboswitch
Archive: https://github.com/yhwang17/Prave-PreQ1_riboswitch/raw/main/plumed.zip
Category: bio
Keywords: ligand, RNA, metadynamics, pRAVE
PLUMED version: 2.5
Contributor: Yihang Wang
Submitted on: 25 Mar 2022
Publication: Y. Wang, S. Parmar, J. S. Schneekloth, P. Tiwary, Interrogating RNA–Small Molecule Interactions with Structure Probing and Artificial Intelligence-Augmented Molecular Simulations. ACS Central Science. 8, 741–748 (2022)
PLUMED input files
Last tested: 18 Mar 2025, 09:48:51
Project description and instructions
The PLUMED files in the production folder can be run with GROMACS 2018.3 using “gmx mdrun md_0_1 -plumed plumed.production.dat”. Please refer to the README file here about how to generate the MD files. The PLUMED files in the analysis folders can be run with “plumed driver –plumed.c-c_distance.dat –mf_xtc md_0_1.xtc”.
Submission history
[v1] 25 Mar 2022: original submission
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