title: Outputs of molecular dynamics simulations of two NS1 ZIKV variants in the membrane presence
author: Poveda Cuevas, Sergio Alejandro
description: Files corresponding to outputs obtained through Molecular Dynamics (MD) simulations of two Non-structural (NS) proteins 1 of the Zika virus from Uganda (ZIKV-UG) and Brazil (ZIKV-BR). Simulations were performed using GROMACS 5.1.5 or later versions.  Systems were built based on atomistic models (https://zenodo.org/record/5608521#.YvDNZTlBzJw) and converted to a coarse-grained representation employing MARTINI 2.2p ElNeDyn. It was assumed to be NS1 systems in apo and holo forms (i.e., in the absence and presence of a lipid bilayer, respectively). The membrane model tries to reproduce a lipid concentration of an endoplasmic reticulum lipid bilayer. Holo and apo systems were simulated until reached 20 and 10 µs, respectively. Trajectories do not include water molecules. For the specific case of holo systems, frames were skipped every 5 frames, which means that processed trajectories are equivalent to simulations when it is recorded every 1000 ps. More details can be found at https://www.biorxiv.org/content/10.1101/2022.04.08.487413v1.full.   Note: Some topology and index files important for MD analysis are also present.