Federal University of Rondônia (UNIR)

1 ARTICLES PUBLISHED IN JoVE

Biochemistry

Ivo Henrique Provensi Vieira^1,2, Esdras Abimael Maia Mendonça^1,2, Fernando Loza Guariero^1,2, Railton Marques de Souza Guimarães^1,2, Fernando Berton Zanchi^1,2,3,4

¹Bioinformatics and Medicinal Chemistry Laboratory (LABIOQUIM), Oswaldo Cruz Rondônia Foundation, ²National Institute of Epidemiology in the Western Amazon - EPIAMO, ³Postgraduate Program in Experimental Biology, Federal University of Rondônia (UNIR), ⁴Doctoral Program in Sciences - IOC/Fiocruz Rondônia Cooperation: Computational Biology and Systems (BCS)

Visual Dynamics is an open-source tool that accelerates implementations and learning in molecular dynamics simulation using Gromacs. The presented protocol will guide you through the steps to perform a protein-ligand simulation prepared in ACPYPE with ease and general steps to other simulation models.