MD simulations of the Sec61/TRAP/ribosome complex Amber force fields

<p>Simulation data for the Sec61/TRAP/ribosome complex&nbsp;embedded in an ER membrane mimic.&nbsp;Simulations are performed using GROMACS and with the all-atom&nbsp;Amber family of force fields. The uploaded trajectory&nbsp;(xtc) contains the coordinates stored every 2 ns of the 2-&micro;s-long simulations. The output energy file&nbsp;(edr), run input file (tpr), and&nbsp;the continue point&nbsp;(cpt) at 2 &micro;s&nbsp;are provided.&nbsp;</p> <p>All required input files are also provided to regenerate the run input file: initial structures (gro), index files (ndx), topologies (top and itp), and the simulation parameter file (mdp).&nbsp; Details of the setup, simulation, and analysis of the systems is available in the preprint:</p> <p>https://doi.org/10.1101/2022.09.30.510141</p>