plumed-eggs

This repository contains archives of data shared on PLUMED-NEST from papers by Jakub Rydzewski jr@fizyka.umk.pl.

All the data and PLUMED input files required to reproduce the results reported in the following papers are available on PLUMED-NEST, the public repository of the PLUMED consortium.

See: The PLUMED consortium: A community effort to promote openness, transparency and reproducibility in molecular simulations, Submitted (2019).

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2019

• J. Rydzewski, maze: Heterogeneous Ligand Unbinding along Transient Protein Tunnels, Comp. Phys. Commun. X, 106865 (2019)

2018

• J. Rydzewski, and O. Valsson, Finding Multiple Reaction Pathways of Ligand Unbinding, J. Chem. Phys. 150, 221101 (2019)

• J. Rydzewski, R. Jakubowski, W. Nowak, and H. Grubmüller, Kinetics of Huperzine A Dissociation from Acetylcholinesterase via Multiple Unbinding Pathways, J. Chem. Theory Comput. 14, 2843 (2018)

2017

• J. Rydzewski, and W. Nowak, Thermodynamics of Camphor Migration in Cytochrome P450cam by Atomistic Simulations, Sci. Rep. 7, 7736 (2017)