Supplementary material for 'Towards a structural identification of metastable molecular conformations'
T. Speck, S. Lemcke, M. Wand, and J. Appeldorn. Software, (2023)Related to: Simon Lemcke, Jörn H. Appeldorn, Michael Wand, Thomas Speck; "Toward a structural identification of metastable molecular conformations", J. Chem. Phys. 21 September 2023; 159 (11): 114105. doi: 10.1063/5.0164145.
DOI: 10.18419/darus-3333
Abstract
This dataset contains simulation input files for GROMACS (topologies, index, simulation parameters, starting frames, run script) to be able to reproduce the data in the mentioned publication. The generated simulation trajectories are given and some processed data: The end-to-end distances for the produced trajectories which are needed for the calculation of free energies. Furthermore two interactive Jupyter notebooks in which the free energy landscape of both of the investigated dimensionality reduction methods TICA and EncoderMap with its respective average structures can be explored. Scripts for setting-up the environment to run these Jupyter-notebooks are provided.
Related to: Simon Lemcke, Jörn H. Appeldorn, Michael Wand, Thomas Speck; "Toward a structural identification of metastable molecular conformations", J. Chem. Phys. 21 September 2023; 159 (11): 114105. doi: 10.1063/5.0164145
%0 Generic
%1 speck2023supplementary
%A Speck, Thomas
%A Lemcke, Simon
%A Wand, Michael
%A Appeldorn, Jörn H.
%D 2023
%K darus ubs_10008 ubs_20014 ubs_30135 unibibliografie
%R 10.18419/darus-3333
%T Supplementary material for 'Towards a structural identification of metastable molecular conformations'
%X This dataset contains simulation input files for GROMACS (topologies, index, simulation parameters, starting frames, run script) to be able to reproduce the data in the mentioned publication. The generated simulation trajectories are given and some processed data: The end-to-end distances for the produced trajectories which are needed for the calculation of free energies. Furthermore two interactive Jupyter notebooks in which the free energy landscape of both of the investigated dimensionality reduction methods TICA and EncoderMap with its respective average structures can be explored. Scripts for setting-up the environment to run these Jupyter-notebooks are provided.
@misc{speck2023supplementary,
abstract = {This dataset contains simulation input files for GROMACS (topologies, index, simulation parameters, starting frames, run script) to be able to reproduce the data in the mentioned publication. The generated simulation trajectories are given and some processed data: The end-to-end distances for the produced trajectories which are needed for the calculation of free energies. Furthermore two interactive Jupyter notebooks in which the free energy landscape of both of the investigated dimensionality reduction methods TICA and EncoderMap with its respective average structures can be explored. Scripts for setting-up the environment to run these Jupyter-notebooks are provided. },
added-at = {2023-06-26T07:11:25.000+0200},
affiliation = {Speck, Thomas/Universität Stuttgart, Lemcke, Simon/Universität Mainz, Wand, Michael/Universität Mainz, Appeldorn, Jörn H./Universität Mainz},
author = {Speck, Thomas and Lemcke, Simon and Wand, Michael and Appeldorn, Jörn H.},
biburl = {https://puma.ub.uni-stuttgart.de/bibtex/233487669c7a0b908a20ad8fdbb6b8ffc/unibiblio},
doi = {10.18419/darus-3333},
howpublished = {Software},
interhash = {69d55bab0a726984539d8ffc0181f350},
intrahash = {33487669c7a0b908a20ad8fdbb6b8ffc},
keywords = {darus ubs_10008 ubs_20014 ubs_30135 unibibliografie},
note = {Related to: Simon Lemcke, Jörn H. Appeldorn, Michael Wand, Thomas Speck; "Toward a structural identification of metastable molecular conformations", J. Chem. Phys. 21 September 2023; 159 (11): 114105. doi: 10.1063/5.0164145},
orcid-numbers = {Speck, Thomas/0000-0002-6357-1180, Lemcke, Simon/0000-0002-0315-3892, Wand, Michael/0009-0004-0509-789X},
timestamp = {2023-09-25T15:16:39.000+0200},
title = {Supplementary material for 'Towards a structural identification of metastable molecular conformations'},
year = 2023
}
