cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.7418618
title: MD Simulation data for a pure DOPC bilayer without salt with AMOEBA force field + OpenMM

description: MD simulation data for the DOPC bilayer with the AMOEBA-based force field developed by Li (https://doi.org/10.1080/00268976.2018.1436201). The simulation contains 72 DOPC lipids and 2880 water molecules. The trajectory is 201,61 ns long (20161 frames with 10 ps saving frequency). <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 12 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.4665772
title: Pure POPE membrane simulations with the CHARMM-Drude force field (OpenMM 7.5.0)

description: MD simulation data of a pure POPE membrane with the CHARMM-Drude force field generated with the OpenMM 7.5.0 simulation engine. All the input parameters are available in the *inp file. The initial structures have been obtained from CHARMM-GUI. Total simulation duration is 300 ns (100 ns x 3, continuing from the last frame, combined with the mdconvert). First 50 ns is discarded as equilibration. This data set contains 300 ns data with 3000 frames (saving frequency is 100 ps). In total, 72 POPC lipids in each leaflet (144 in total), 5040 SWM4-NPD water molecules. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the previously uploaded trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "unwrapped_all_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 100 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 3 sub-trajectories, each of which starts from the last frame of the previous one. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.3994330
title: Pure POPC Membrane with 650mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 76 CaCl2, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. The initial structures have been obtained from CHARMM-GUI. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.3994320
title: Pure POPC Membrane with 350mM CaCl2 simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 41 CaCl2, and 6400 SWM4 water molecules. wrapped.dcd has a frame saving frequency of 100 ps. Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.3991506
title: Pure POPC Membrane with 1000mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 115 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.3991894
title: Pure POPC Membrane with 650mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 77 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.3991896
title: Pure POPC Membrane with 450mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 51 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.3991902
title: Pure POPC Membrane with 350mM NaCl simulations using Drude Polarizable Force Field and OpenMM

description: 500 ns MD simulation of pure POPC membrane using Charmm-Drude polarizable force field. The system contains 128 POPC lipids, 41 NaCl, and 6400 SWM4 water molecules. The simulation have been performed using OpenMM 7.4.1 Before running the Drude simulation, the system has been equilibriated using Charmm36 force field for 200 ns. The last frame of that simulation was used to generate Drude polarizable model. The first 100 ns of the Drude simulation has been discarded from this dataset. wrapped.dcd has a frame saving frequency of 100 ps. <strong>It has been discovered that (https://github.com/NMRLipids/Databank/issues/2#issuecomment-1357871243) the wrapped_full.dcd trajectory did not have the correct timestamp: the timestep between two consecutive simulation frames was not correctly embedded into the trajectory information. Therefore, with the latest version we are uploading the "wrapped_full_fixed_dt.xtc" which has the correct timestamp. The frame saving frequency in this trajectory is 10 ps. </strong> <strong>This new update should not invalidate any previous calculations that did not explicitly read the timestamp information from the trajectory.</strong> <strong>This simulation consists of 5 sub-trajectories, each of which starts from the last frame of the previous one and runs for 100 ns. These trajectories (originally in dcd format) were concatenated and saved in xtc format with MDAnalysis.</strong>
DOI: 10.5281/zenodo.7607041
title: mapping

description: dasfa ea gaegae gaegaeg
DOI: 10.6084/m9.figshare.22012373
title: Untitled ItemEffectiveness of a community-based intervention (Konga model) to address the factors contributing to low viral load suppression among children living with HIV in Tanzania: A cluster-randomized clinical trial dataset

description: This data comes from a randomised controlled trial to evaluate the effectiveness of a community-based intervention (Konga model) in addressing the factors contributing to low viral load suppression among children living with HIV in the Simiyu region, Tanzania. Upon completing our data analyses, the Konga model demonstrated significant positive effects that improved viral load suppression. We recommend that you implement the Konga model trial in other regions to improve the consistency of the results; later, it can be used elsewhere. Our study contributes significantly to the literature, demonstrating that a community-based organisation (Konga) effectively improves viral load among children receiving ART. Further, we believe that this data will be of interest to the readership of your repository because our data increases our current understanding of the social dimensions of HIV in an African context and provides recommendations related to improving HIV care, particularly for children.
DOI: 10.5517/ccdc.csd.cc2cpsgb
title: CCDC 2195682: Experimental Crystal Structure Determination

description: Related Article: Deepak Manoharan, S. N. Megha, Mangalampalli S. R. N. Kiran, Franziska Emmerling, Biswajit Bhattacharya, Soumyajit Ghosh|2023|Cryst.Growth Des.|23|657|doi:10.1021/acs.cgd.2c01137
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cpshc
title: CCDC 2195683: Experimental Crystal Structure Determination

description: Related Article: Deepak Manoharan, S. N. Megha, Mangalampalli S. R. N. Kiran, Franziska Emmerling, Biswajit Bhattacharya, Soumyajit Ghosh|2023|Cryst.Growth Des.|23|657|doi:10.1021/acs.cgd.2c01137
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cpsjd
title: CCDC 2195684: Experimental Crystal Structure Determination

description: Related Article: Deepak Manoharan, S. N. Megha, Mangalampalli S. R. N. Kiran, Franziska Emmerling, Biswajit Bhattacharya, Soumyajit Ghosh|2023|Cryst.Growth Des.|23|657|doi:10.1021/acs.cgd.2c01137
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2cpskf
title: CCDC 2195685: Experimental Crystal Structure Determination

description: Related Article: Deepak Manoharan, S. N. Megha, Mangalampalli S. R. N. Kiran, Franziska Emmerling, Biswajit Bhattacharya, Soumyajit Ghosh|2023|Cryst.Growth Des.|23|657|doi:10.1021/acs.cgd.2c01137
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d4l9g
title: CCDC 2208945: Experimental Crystal Structure Determination

description: Related Article: Jiyao Yu, John Bacsa, Christoph J. Fahrni|2023|Inorg.Chem.|62|1287|doi:10.1021/acs.inorgchem.2c03524
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d4lbh
title: CCDC 2208946: Experimental Crystal Structure Determination

description: Related Article: Jiyao Yu, John Bacsa, Christoph J. Fahrni|2023|Inorg.Chem.|62|1287|doi:10.1021/acs.inorgchem.2c03524
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d4lcj
title: CCDC 2208947: Experimental Crystal Structure Determination

description: Related Article: Jiyao Yu, John Bacsa, Christoph J. Fahrni|2023|Inorg.Chem.|62|1287|doi:10.1021/acs.inorgchem.2c03524
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d4ldk
title: CCDC 2208948: Experimental Crystal Structure Determination

description: Related Article: Jiyao Yu, John Bacsa, Christoph J. Fahrni|2023|Inorg.Chem.|62|1287|doi:10.1021/acs.inorgchem.2c03524
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d5m3b
title: CCDC 2209931: Experimental Crystal Structure Determination

description: Related Article: Tiantian Li, Han Xiao, Renjun Tian, Jilan Wang, Yingchun Luo, Qingyun Wang, Shuquan Wu, Pengcheng Zheng|2023|Org.Lett.|25|688|doi:10.1021/acs.orglett.2c04340
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d64g7
title: CCDC 2210438: Experimental Crystal Structure Determination

description: Related Article: Tiantian Li, Han Xiao, Renjun Tian, Jilan Wang, Yingchun Luo, Qingyun Wang, Shuquan Wu, Pengcheng Zheng|2023|Org.Lett.|25|688|doi:10.1021/acs.orglett.2c04340
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d88lk
title: CCDC 2212488: Experimental Crystal Structure Determination

description: Related Article: Leonardo Tensi, Anna Dall’Anese, Alfonso Annunziata, Simone Mearini, Vittorio Nofrini, Gabriel Menendez Rodriguez, Andrea Carotti, Roccaldo Sardella, Francesco Ruffo, Alceo Macchioni|2023|Organometallics|42|157|doi:10.1021/acs.organomet.2c00544
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d88ml
title: CCDC 2212489: Experimental Crystal Structure Determination

description: Related Article: Leonardo Tensi, Anna Dall’Anese, Alfonso Annunziata, Simone Mearini, Vittorio Nofrini, Gabriel Menendez Rodriguez, Andrea Carotti, Roccaldo Sardella, Francesco Ruffo, Alceo Macchioni|2023|Organometallics|42|157|doi:10.1021/acs.organomet.2c00544
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2d88nm
title: CCDC 2212490: Experimental Crystal Structure Determination

description: Related Article: Leonardo Tensi, Anna Dall’Anese, Alfonso Annunziata, Simone Mearini, Vittorio Nofrini, Gabriel Menendez Rodriguez, Andrea Carotti, Roccaldo Sardella, Francesco Ruffo, Alceo Macchioni|2023|Organometallics|42|157|doi:10.1021/acs.organomet.2c00544
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dgw0s
title: CCDC 2218825: Experimental Crystal Structure Determination

description: Related Article: Neng Wang, Hang Wang, Lin-Xi Wan, Xiao-Huan Li, Xian-Li Zhou, Jia-Hong Li, Steven De Jonghe, Dominique Schols, Jin-Bu Xu, Feng Gao|2023|Org.Lett.|25|597|doi:10.1021/acs.orglett.2c04116
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2dmp6y
title: CCDC 2223450: Experimental Crystal Structure Determination

description: Related Article: Monika Warzecha, Alan R. Kennedy, Callum J. McHugh, Jesus Calvo-Castro|2023|Cryst.Growth Des.|23|670|doi:10.1021/acs.cgd.2c01420
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
DOI: 10.5517/ccdc.csd.cc2f1r4d
title: CCDC 2236003: Experimental Crystal Structure Determination

description: Related Article: Tiantian Li, Han Xiao, Renjun Tian, Jilan Wang, Yingchun Luo, Qingyun Wang, Shuquan Wu, Pengcheng Zheng|2023|Org.Lett.|25|688|doi:10.1021/acs.orglett.2c04340
description: An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.