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

File Compatible with
plumed/6e1u/analysis/plumed.c-c_distance.dat tested on v2.8 tested on master
plumed/6e1u/production/plumed.production.dat tested on v2.8 tested on master
plumed/6e1w/analysis/plumed.c-c_distance.dat tested on v2.8 tested on master
plumed/6e1w/production/plumed.production.dat tested on v2.8 tested on master
plumed/apo/analysis/plumed.c-c_distance.dat tested on v2.8 tested on master

Last tested: 22 Jun 2022, 17:13:14

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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plumeDnest:22.013