{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/753b9d09d18ad3c88a38a4461d2e6ca8/diglezakis", "tags" : [ "forschungsdaten","materialien","metadata","simulations","materialwissenschaften","repository" ], "intraHash" : "753b9d09d18ad3c88a38a4461d2e6ca8", "label" : "Virtual Materials Marketplace \u2013 VIMMP", "user" : "diglezakis", "description" : "VIMMP provides an easily accessible, user-friendly hub to access all tangible and intangible components, such as information, knowledge, services and tools to support the efficient decision making, uptake and effective use of materials. At the core of VIMMP will be a metadata enriched data environment that eases the tasks of all actors. In particular it will facilitate the translation of a scientific problem into modelling workflows, ready for simulation using a range of software tools integrated into an open simulation platform and deployed on cloud services. The VIMMP platform is open, so that any provider can easily integrate and deploy their software codes as well as services.", "date" : "2020-03-10 10:42:42", "changeDate" : "2020-03-10 09:42:42", "count" : 1, "url" : "https://www.vimmp.eu/" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2714dca46376651961024e72878db421e/diglezakis", "tags" : [ "simulations","tools" ], "intraHash" : "714dca46376651961024e72878db421e", "interHash" : "07b8aade355592acdee2e9d30dfeefe2", "label" : "High performance cellular level agent-based simulation with FLAME for the GPU", "user" : "diglezakis", "description" : "", "date" : "2023-04-27 07:50:40", "changeDate" : "2023-04-27 07:50:40", "count" : 2, "pub-type": "article", "journal": "Briefings in bioinformatics","publisher":"Oxford Univ Press", "year": "2010", "url": "", "author": [ "Paul Richmond","Dawn Walker","Simon Coakley","Daniela Romano" ], "authors": [ {"first" : "Paul", "last" : "Richmond"}, {"first" : "Dawn", "last" : "Walker"}, {"first" : "Simon", "last" : "Coakley"}, {"first" : "Daniela", "last" : "Romano"} ], "volume": "11","number": "3","pages": "334--347", "doi" : "10.1093/bib/bbp073", "bibtexKey": "richmond2010high" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/2302ba3131b9154c3d32d522413c6fb6a/diglezakis", "tags" : [ "forschungsdaten","motivation","reproducibility","chemistry","simulations","thermodynamics" ], "intraHash" : "302ba3131b9154c3d32d522413c6fb6a", "interHash" : "0c9228faa4ec9bc0de45981d5be060db", "label" : "Round Robin Study: Molecular Simulation of Thermodynamic Properties from Models with Internal Degrees of Freedom", "user" : "diglezakis", "description" : "Kernfrage:\r\nHow reproducible is information on a quantity xmod defined by a model, which is only accessible by computer simulation, if different codes are used?", "date" : "2018-12-03 14:28:07", "changeDate" : "2020-01-07 08:39:29", "count" : 1, "pub-type": "article", "journal": "Journal of Chemical Theory and Computation", "year": "2017", "url": "https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00489", "author": [ "Michael Schappals","Andreas Mecklenfeld","Leif Kröger","Vitalie Botan","Andreas Köster","Simon Stephan","Edder J. García","Gabor Rutkai","Gabriele Raabe","Peter Klein","Kai Leonhard","Colin W. Glass","Johannes Lenhard","Jadran Vrabec","Hans Hasse" ], "authors": [ {"first" : "Michael", "last" : "Schappals"}, {"first" : "Andreas", "last" : "Mecklenfeld"}, {"first" : "Leif", "last" : "Kröger"}, {"first" : "Vitalie", "last" : "Botan"}, {"first" : "Andreas", "last" : "Köster"}, {"first" : "Simon", "last" : "Stephan"}, {"first" : "Edder J.", "last" : "García"}, {"first" : "Gabor", "last" : "Rutkai"}, {"first" : "Gabriele", "last" : "Raabe"}, {"first" : "Peter", "last" : "Klein"}, {"first" : "Kai", "last" : "Leonhard"}, {"first" : "Colin W.", "last" : "Glass"}, {"first" : "Johannes", "last" : "Lenhard"}, {"first" : "Jadran", "last" : "Vrabec"}, {"first" : "Hans", "last" : "Hasse"} ], "volume": "13","number": "9","pages": "4270-4280","note": "PMID: 28738147","abstract": "Thermodynamic properties are often modeled by classical force fields which describe the interactions on the atomistic scale. Molecular simulations are used for retrieving thermodynamic data from such models, and many simulation techniques and computer codes are available for that purpose. In the present round robin study, the following fundamental question is addressed: Will different user groups working with different simulation codes obtain coinciding results within the statistical uncertainty of their data? A set of 24 simple simulation tasks is defined and solved by five user groups working with eight molecular simulation codes: DL_POLY, GROMACS, IMC, LAMMPS, ms2, NAMD, Tinker, and TOWHEE. Each task consists of the definition of (1) a pure fluid that is described by a force field and (2) the conditions under which that property is to be determined. The fluids are four simple alkanes: ethane, propane, n-butane, and iso-butane. All force fields consider internal degrees of freedom: OPLS, TraPPE, and a modified OPLS version with bond stretching vibrations. Density and potential energy are determined as a function of temperature and pressure on a grid which is specified such that all states are liquid. The user groups worked independently and reported their results to a central instance. The full set of results was disclosed to all user groups only at the end of the study. During the study, the central instance gave only qualitative feedback. The results reveal the challenges of carrying out molecular simulations. Several iterations were needed to eliminate gross errors. For most simulation tasks, the remaining deviations between the results of the different groups are acceptable from a practical standpoint, but they are often outside of the statistical errors of the individual simulation data. However, there are also cases where the deviations are unacceptable. This study highlights similarities between computer experiments and laboratory experiments, which are both subject not only to statistical error but also to systematic error.", "eprint" : "https://doi.org/10.1021/acs.jctc.7b00489", "doi" : "10.1021/acs.jctc.7b00489", "bibtexKey": "doi:10.1021/acs.jctc.7b00489" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/288c2137872d98a95c68ad329a304e1e4/diglezakis", "tags" : [ "forschungsdaten","metadata","simulations" ], "intraHash" : "88c2137872d98a95c68ad329a304e1e4", "interHash" : "5a35352d31a7f5172f513975262120c4", "label" : "Standards-based metadata management for molecular simulations", "user" : "diglezakis", "description" : "Standards-based metadata management for molecular simulations - Grunzke - 2013 - Concurrency and Computation: Practice and Experience - Wiley Online Library", "date" : "2017-08-21 13:33:48", "changeDate" : "2017-08-21 11:33:48", "count" : 3, "pub-type": "article", "journal": "Concurrency and Computation: Practice and Experience", "year": "2014", "url": "http://dx.doi.org/10.1002/cpe.3116", "author": [ "Richard Grunzke","Sebastian Breuers","Sandra Gesing","Sonja Herres-Pawlis","Martin Kruse","Dirk Blunk","Luis de la Garza","Lars Packschies","Patrick Schäfer","Charlotta Schärfe","Tobias Schlemmer","Thomas Steinke","Bernd Schuller","Ralph Müller-Pfefferkorn","René Jäkel","Wolfgang E. Nagel","Malcolm Atkinson","Jens Krüger" ], "authors": [ {"first" : "Richard", "last" : "Grunzke"}, {"first" : "Sebastian", "last" : "Breuers"}, {"first" : "Sandra", "last" : "Gesing"}, {"first" : "Sonja", "last" : "Herres-Pawlis"}, {"first" : "Martin", "last" : "Kruse"}, {"first" : "Dirk", "last" : "Blunk"}, {"first" : "Luis", "last" : "de la Garza"}, {"first" : "Lars", "last" : "Packschies"}, {"first" : "Patrick", "last" : "Schäfer"}, {"first" : "Charlotta", "last" : "Schärfe"}, {"first" : "Tobias", "last" : "Schlemmer"}, {"first" : "Thomas", "last" : "Steinke"}, {"first" : "Bernd", "last" : "Schuller"}, {"first" : "Ralph", "last" : "Müller-Pfefferkorn"}, {"first" : "René", "last" : "Jäkel"}, {"first" : "Wolfgang E.", "last" : "Nagel"}, {"first" : "Malcolm", "last" : "Atkinson"}, {"first" : "Jens", "last" : "Krüger"} ], "volume": "26","number": "10","pages": "1744--1759","abstract": "State-of-the-art research in a variety of natural sciences depends heavily on methods of computational chemistry, for example, the calculation of the properties of materials, proteins, catalysts, and drugs. Applications providing such methods require a lot of expertise to handle their complexity and the usage of high-performance computing. The MoSGrid (molecular simulation grid) infrastructure relieves this burden from scientists by providing a science gateway, which eases access to and usage of computational chemistry applications. One of its cornerstones is the molecular simulations markup language (MSML), an extension of the chemical markup language. MSML abstracts all chemical as well as computational aspects of simulations. An application and its results can be described with common semantics. Using such application, independent descriptions users can easily switch between different applications or compare them. This paper introduces MSML, its integration into a science gateway, and its usage for molecular dynamics, quantum chemistry, and protein docking. Copyright © 2013 John Wiley & Sons, Ltd.", "issn" : "1532-0634", "doi" : "10.1002/cpe.3116", "bibtexKey": "CPE:CPE3116" } ] }