Project ID: plumID:22.036
Name: Well-tempered MetaDynamics with Hamiltonian Replica Exchange on Holliday Junction
Category: bio
Keywords: Well-tempered MetaDynamics with Hamiltonian Replica Exchange
PLUMED version: 2.5.6
Contributor: Miroslav Krepl
Submitted on: 24 Sep 2022
Publication: Z. Zhang, J. Šponer, G. Bussi, V. Mlýnský, P. Šulc, C. R. Simmons, N. Stephanopoulos, M. Krepl, Atomistic Picture of Opening–Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations. Journal of Chemical Information and Modeling. 63, 2794–2809 (2023)

PLUMED input files

File Compatible with
plumed.dat tested on v2.9 tested on master with LOAD

Last tested: 26 Feb 2024, 07:18:45

Project description and instructions
Detailed instruction under README.dat file. The topology and coordinate files were prepared in AMBER18, proceeded by ParmED. Then, they were converted to GROMACS format by ParmED. GROMACS-v2018 and PLUMED-v2.5.6 were used for the WT-MetaD-HREX simulations, and the latter was also used for data processing.

Submission history
[v1] 24 Sep 2022: original submission

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