Supplementary material for 'Towards a structural identification of metastable molecular conformations'

DOI

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. Jupyter notebooks are given which use the raw data and follow the modeling pipeline to the Markov state modeling step. Latent spaces including training EncoderMap can be reproduced this way as well as the respective MSMs. 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.

Identifier
DOI https://doi.org/10.18419/darus-3333
Related Identifier IsCitedBy https://doi.org/10.1063/5.0164145
Metadata Access https://darus.uni-stuttgart.de/oai?verb=GetRecord&metadataPrefix=oai_datacite&identifier=doi:10.18419/darus-3333
Provenance
Creator Speck, Thomas ORCID logo; Lemcke, Simon ORCID logo; Wand, Michael (ORCID: 0009-0004-0509-789X); Appeldorn, Jörn H.
Publisher DaRUS
Contributor Speck, Thomas
Publication Year 2023
Funding Reference DFG TRR 146 - 404840447 ; Carl-Zeiss-Stiftung Emergent AI Center ; Rhineland-Palatinate Research Initiative Mainz Institute of Multiscale Modeling (M³ODEL)
Rights info:eu-repo/semantics/openAccess
OpenAccess true
Contact Speck, Thomas (Universität Stuttgart)
Representation
Resource Type Dataset
Format application/gzip; application/x-gzip; text/plain
Size 5385779; 252792515; 11210; 504542440; 2472; 45117318
Version 2.0
Discipline Natural Sciences; Physics
Spatial Coverage University of Mainz