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The molecular dynamics simulation softwares are very useful, however, most of them are used in command line form and continue with the same common implementation difficulties that plague researchers who are not computer specialists.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Here, we have developed the VisualDynamics\u2014a WEB tool developed to automate biological simulations performed in Gromacs using a graphical interface to make molecular dynamics simulation user-friendly task. In this new application the researcher can submit a simulation of the protein in the free form or complexed with a ligand. Can also download the graphics analysis and log files at the end of the simulation.\n<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>VisualDynamics is a tool that will accelerate implementations and learning in the area of molecular dynamics simulation. Freely available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/visualdynamics.fiocruz.br\/login\">https:\/\/visualdynamics.fiocruz.br\/login<\/jats:ext-link>, is supported by all major web browsers. VisualDynamics was developed with Flask, which is a Python-based free and open-source framework for web development. The code is freely available for download at GitHub <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"https:\/\/github.com\/LABIOQUIM\/visualdynamics\">https:\/\/github.com\/LABIOQUIM\/visualdynamics<\/jats:ext-link>.\n<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12859-023-05234-y","type":"journal-article","created":{"date-parts":[[2023,3,26]],"date-time":"2023-03-26T21:15:36Z","timestamp":1679865336000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":120,"title":["Visual dynamics: a WEB application for molecular dynamics simulation using GROMACS"],"prefix":"10.1186","volume":"24","author":[{"given":"Ivo Henrique Provensi","family":"Vieira","sequence":"first","affiliation":[]},{"given":"Eduardo Buganemi","family":"Botelho","sequence":"additional","affiliation":[]},{"given":"Thales Junior","family":"de Souza Gomes","sequence":"additional","affiliation":[]},{"given":"Roger","family":"Kist","sequence":"additional","affiliation":[]},{"given":"Rafael Andrade","family":"Caceres","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3386-0069","authenticated-orcid":false,"given":"Fernando Berton","family":"Zanchi","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2023,3,22]]},"reference":[{"issue":"5","key":"5234_CR1","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1021\/cr040426m","volume":"106","author":"SA Adcock","year":"2006","unstructured":"Adcock SA, McCammon JA. 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