title: MDWiZ: a platform for the automated translation of molecular dynamics simulations.
abstract: A variety of popular molecular dynamics (MD) simulation packages were independently developed in the last decades to reach diverse scientific goals. However, such non-coordinated development of software, force fields, and analysis tools for molecular simulations gave rise to an array of software formats and arbitrary conventions for routine preparation and analysis of simulation input and output data. Different formats and/or parameter definitions are used at each stage of the modeling process despite largely contain redundant information between alternative software tools. Such Babel of languages that cannot be easily and univocally translated one into another poses one of the major technical obstacles to the preparation, translation, and comparison of molecular simulation data that users face on a daily basis. Here, we present the MDWiZ platform, a freely accessed online portal designed to aid the fast and reliable preparation and conversion of file formats that allows researchers to reproduce or generate data from MD simulations using different setups, including force fields and models with different underlying potential forms. The general structure of MDWiZ is presented, the features of version 1.0 are detailed, and an extensive validation based on GROMACS to LAMMPS conversion is presented. We believe that MDWiZ will be largely useful to the molecular dynamics community. Such fast format and force field exchange for a given system allows tailoring the chosen system to a given computer platform and/or taking advantage of a specific capabilities offered by different software engines.
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil.
authors.forename: Victor H
authors.initials: VH
authors.lastname: Rusu
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA; Department of Computational Sciences, Federal University of Juiz de Fora, Juiz de Fora, Brazil.
authors.forename: Vitor A C
authors.initials: VA
authors.lastname: Horta
authors.affiliation: Department of Electrical Engineering, Pontíficia Universidade Católica do Rio de Janeiro, Rio de Janeiro, Brazil; Department of Biotechnology and Biological Sciences, Centro Universitário Estadual da Zona Oeste, Rio de Janeiro, Brazil.
authors.forename: Bruno A C
authors.initials: BA
authors.lastname: Horta
authors.affiliation: Department of Fundamental Chemistry, Federal University of Pernambuco, Cidade Universitária, Recife, PE 50740-560, Brazil.
authors.forename: Roberto D
authors.initials: RD
authors.lastname: Lins
authors.affiliation: Department of Medicinal Chemistry, College of Pharmacy, and The Henry Eyring Center for Theoretical Chemistry, The University of Utah, Salt Lake City, UT 84112-5820, USA. Electronic address: r.baron@utah.edu.
authors.forename: Riccardo
authors.initials: R
authors.lastname: Baron
mesh_terms: D000081:Acetamides / Q000737:chemistry; D000409:Alanine / Q000737:chemistry; D000465:Algorithms; D000473:Alkanes / Q000737:chemistry; D020134:Catalytic Domain; D004151:Dipeptides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D009113:Muramidase / Q000737:chemistry; D017433:Protein Structure, Secondary; D012984:Software
chemical_list: D000081:Acetamides; D000473:Alkanes; D004151:Dipeptides; D009113:Muramidase; D000409:Alanine; C018595:N-methylacetamide
keywords: Force field; Language barrier; MD Wizard; Molecular simulation; Software; Validation