# SARS-CoV-2 main protease (apo, monomer) Folding@home simulations ## Main project repository All code used to set up the simulations can be found on Github here: https://github.com/FoldingAtHome/coronavirus/tree/master/system-preparation/6lu7_receptor ## Trajectories without solvent Folding@home projects **11743 and 11749** are made available here without solvent, but including salt. Both of these projects were initiated from PDB structure [**6lu7**][3], chain A (after removing the inhibitor (i.e. in **apo** form), as a **monomer**). The split into two projects is simply the result of the architecture of Folding@home, there are no differences in the setups between these projects. Please note the identical file names in both projects, there is no relation between the identically named files - all trajectories are initialized with different random velocities. Each trajectory is available in the appropriate project folder with trajectory files formatted as `run<RUN>-clone<CLONE>.h5`, with `<RUN>` indexing a set of trajectories started from the same conformation (i.e. all trajectories here are `RUN0`) and `<CLONE>` denoting different replicates initiated from the same structure but different initial velocities. These trajectories are stored in [MDTraj HDF5 format][1]. This is a compact, platform-portable format that contains both topology information (atom names, connectivity, and residue information) and trajectory data. You can use the freely-available [MDTraj][2] package to convert to other popular trajectory formats. [1]: http://mdtraj.org/latest/hdf5_format.html [2]: http://mdtraj.org [3]: http://www.rcsb.org/structure/6LU7