Molecular Dynamics Trajectories of SARS-CoV-2 S and ACE2: WT and N501Y
Description
This dataset has molecular dynamics trajectories of SARS-CoV-2 RBD and ACE2 apo and holo as extracted from PDB 6m0j. The dataset is divided into 3 subfolders: ACE2, WT, and N501Y. WT and N501Y each have apo and holo subfolders. Each system is presented as 3 replicas.
Files
Steps to reproduce
For this work we modeled five distinct systems: sRBD, sRBD_N501Y, sACE2, sRBD:sACE2, and sRBD_N501Y:sACE2. All atomic coordinates were based on the PDB entry 6M0J. All systems were solvated in explicit TIP3P water and neutralized with counterions. Equilibrium MD simulations were run using NAMD for 40 ns. Three replicas of each system were simulated. All systems utilized periodic boundary conditions, a nonbonded cutoff of 11AA, a particle-mesh Ewald grid spacing of 1AA, and a timestep of 2fs. All simulations were conducted at 310K using a Langevin themostat with a friction parameter of 5ps^-1.