MD simulations of the Sec61/TRAP/ribosome complex and various subcomplexes with CHARMM36 force field

<p>Simulation data for the Sec61/TRAP/ribosome complex and its subcomplexes (TRAP alone, Sec61 alone, as well as Sec61 with TRAP) embedded in an ER membrane mimic.&nbsp;Simulations are performed using GROMACS and with the all-atom&nbsp;CHARMM family of force fields. The uploaded trajectories&nbsp;(xtc) contain&nbsp;the coordinates stored every 2 ns of the 2-&micro;s-long simulations. The output energy files (edr), run input files (tpr), and&nbsp;the continue points&nbsp;(cpt) at 2 &micro;s&nbsp;are provided.&nbsp;</p> <p>This upload also contains data for the Sec61/TRAP/ribosome complex simulated in a POPC bicelle. This simulation is 1 &micro;s long and the coordinates are stored every 1 ns.</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> <p>&nbsp;</p>