cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.14830316
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the WQ RFPS-AIMMD and AIMMD runs

description: This repository contains the trajectory files for the RFPS-AIMMD and AIMMD runs of the WQ system. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- wq   |- fps0 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...   |- fps1   |- ...   |- fps9   |- tps0 (the AIMMD run, with TPS for the shooting simulations)      |- ...   |- tps1   |- ...   |- tps9
DOI: 10.5281/zenodo.14830317
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the WQ RFPS-AIMMD and AIMMD runs

description: This repository contains the trajectory files for the RFPS-AIMMD and AIMMD runs of the WQ system. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- wq   |- fps0 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...   |- fps1   |- ...   |- fps9   |- tps0 (the AIMMD run, with TPS for the shooting simulations)      |- ...   |- tps1   |- ...   |- tps9
DOI: 10.5281/zenodo.14830279
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin AIMMD run "tps2"

description: This repository contains the trajectory files for the AIMMD run "tps2" of chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- tps2 (the AIMMD run, with TPS for the shooting simulations)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830280
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin AIMMD run "tps2"

description: This repository contains the trajectory files for the AIMMD run "tps2" of chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- tps2 (the AIMMD run, with TPS for the shooting simulations)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830269
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin AIMMD run "tps1"

description: This repository contains the trajectory files for the AIMMD run "tps1" of chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- tps1 (the AIMMD run, with TPS for the shooting simulations)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830270
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin AIMMD run "tps1"

description: This repository contains the trajectory files for the AIMMD run "tps1" of chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- tps1 (the AIMMD run, with TPS for the shooting simulations)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830250
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin AIMMD run "tps0"

description: This repository contains the trajectory files for the AIMMD run "tps0" of chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- tps0 (the AIMMD run, with TPS for the shooting simulations)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830251
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin AIMMD run "tps0"

description: This repository contains the trajectory files for the AIMMD run "tps0" of chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- tps0 (the AIMMD run, with TPS for the shooting simulations)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830223
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin RFPS-AIMMD run "fps2"

description: This repository contains the trajectory files of the RFPS-AIMMD run "fps2" on chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- fps2 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830224
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin RFPS-AIMMD run "fps2"

description: This repository contains the trajectory files of the RFPS-AIMMD run "fps2" on chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- fps2 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830199
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin RFPS-AIMMD run "fps1"

description: This repository contains the trajectory files of the RFPS-AIMMD run "fps1" on chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- fps1 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14830200
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin RFPS-AIMMD run "fps1"

description: This repository contains the trajectory files of the RFPS-AIMMD run "fps1" on chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- fps1 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14826022
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin RFPS-AIMMD run "fps0"

description: This repository contains the trajectory files of the RFPS-AIMMD run "fps0" on chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- fps0 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.5281/zenodo.14826023
title: Simulation data for "Optimal Rejection-Free Path Sampling". Trajectory files of the chignolin RFPS-AIMMD run "fps0"

description: This repository contains the trajectory files of the RFPS-AIMMD run "fps0" on chignolin. It includes the two-way shooting paths and the free simulations around state A and state B. 

Due to size constraints, the data has been split into separate repositories. 

The trajectory files are not required for running the main analysis, as all necessary information for machine learning and path reweighting is contained in the "PatEnsemble" object files stored in the main repository. However, these trajectories are essential for projecting the path ensemble estimate onto an arbitrary set of collective variables.

To reconstruct the full dataset, please merge the data folder from the main repository with the one you find here.

Data structure and content

data|- chignolin   |- fps0 (the RFPS-AIMMD run)      |- equilibriumA (the trajectory data for the free simulations around A)         |- traj000001.part0000.xtc         |- traj000001.part0001.xtc         |- ...         |- traj000002.part0000.xtc         |- ...      |- equilibriumB (the trajectory data for the free simulations around B)         |- ...      |- shots0 (the path sampling chain, with the paths in order)         |- path000001.xtc         |- path000002.xtc         |- ...
DOI: 10.15468/dl.smne2b
title: Occurrence Download

description: A dataset containing 8805 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is one of (Europe, Asia)",
 "CoordinateUncertaintyInMeters 0.0-500.0",
 "Geometry POLYGON((14 38,65 38,65 72,14 72,14 38))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is one of (Chamaecytisus ruthenicus (Fisch. ex Wol.) Klásk., Dianthus borbasii Vandas, Jurinea cyanoides (L.) Rchb., Koeleria glauca (Spreng.) DC.)"
 ]
}

 The dataset includes 8805 records from 81 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000899-250325103851331/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.3535/p9n-kwg-x7m
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/yfw-5yv-jk3
title: Jalmenus evagoras (Donovan, 1805)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-zsw-qbga
title: PAN-00140899 - tubular cloth seal

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00140899&lt;/p&gt;
description: Modified: 2023-11-07T15:58:57+01:00
DOI: 10.3535/6ma-87p-xhg
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/t7m-y1w-zvz
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/069-6eb-l49
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-zsw-rdn5
title: PAN-00129386 - fragment hair pin / dress pin

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00129386&lt;/p&gt;
description: Modified: 2023-04-11T10:24:15+02:00
DOI: 10.3535/8dc-393-5e1
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/w9t-8aq-eyx
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/6n6-w9b-fym
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/7ql-jjl-m6c
title: Luthrodes cleotas (Guérin-Méneville, 1829)

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-zsw-rukc
title: PAN-00109822 - Late Antique stylus type V

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00109822&lt;/p&gt;
description: Modified: 2023-04-27T15:57:29+02:00
DOI: 10.3535/hlb-0a3-101
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/jxl-f17-cp5
title: Zygaena (Agrumenia) fausta Linnaeus, 1767

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/3vb-s5e-c9c
title: Parnassius

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/grw-hfw-4sz
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.17026/dans-zsw-ryex
title: PAN-00079560 - finger ring group 2

description: &lt;p&gt;This find is registered at Portable Antiquities of the Netherlands with number PAN-00079560&lt;/p&gt;
description: Modified: 2023-05-09T14:14:12+02:00
DOI: 10.3535/ga1-zlc-2nh
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/j9c-z8r-n40
title: Lepidoptera Linnaeus, 1758

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.
DOI: 10.3535/dkt-2h6-f4x
title: Animalia

description: Digital Specimen for the physical specimen hosted at Naturalis Biodiversity Center.