PLUMED-NEST

Project ID: plumID:23.006
Name: Transcription factor unbinding
Archive: https://github.com/mallu2/Transcriptionfactor_unbinding/archive/main.zip (browse)
Category: bio
Keywords: metadynamics, DNA, conformational changes
PLUMED version: 2.7.2
Contributor: Malin Lüking
Submitted on: 15 Feb 2023
Publication: M. Lüking, D. van der Spoel, J. Elf, G. A. Tribello, Can molecular dynamics be used to simulate biomolecular recognition? The Journal of Chemical Physics. 158 (2023)

PLUMED input files

File	Compatible with
1OSL_CV_analsyis/plumed_print.dat
1OSL_CV_analsyis/plumed_print_1efa.dat
1OSL_CV_analsyis/plumed_print_1osl.dat
…LUMED_input/PLUMED_files/NMR_1osl/plumed_print.dat
…_input/PLUMED_files/NOD/alphaRMSD/plumed_print.dat
…ED_input/PLUMED_files/NOD/alphaRMSD/plumed_run.dat
…ut/PLUMED_files/OSymL/DNA_bending/plumed_print.dat
…nput/PLUMED_files/OSymL/DNA_bending/plumed_run.dat
…nput/PLUMED_files/OSymL/alphaRMSD/plumed_print.dat
…_input/PLUMED_files/OSymL/alphaRMSD/plumed_run.dat
…PLUMED_files/OSymL/hinge_contacts/plumed_print.dat
…t/PLUMED_files/OSymL/hinge_contacts/plumed_run.dat
…input/PLUMED_files/OSymL/specific/plumed_print.dat
…D_input/PLUMED_files/OSymL/specific/plumed_run.dat

Last tested: 07 Oct 2024, 17:33:07

Project description and instructions
This repository contains the starting structures and GROMACS input files to run conventional molecular dynamics simulations, MD simulations with NMR restraints and metadynamics on a complex between the transcription factor LacI and different sequences of DNA.

Submission history
[v1] 15 Feb 2023: original submission

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