MD preview and settings for: "Secondary Chelation through Shared Water Provides Ion Selectivity in Bacterial Sodium Channels"

This repository contains MD setup files for several simulations, as well as parts of two MD trajectories from the paper entitled “Secondary Chelation through Shared Water Provides Ion Selectivity in Bacterial Sodium Channels”. Where only setup files available, there are topologies, MD settings (*.mdp), index files (*.ndx) and initial structure files prior to production, but after equilibration runs (*.gro).

Archives contain:

free_MD_amber.zip: free MD at Vtm = −100 mV. In this large archive, also 500 ns fragments of main MD trajectories with Na+ and K+ are also included; ion passage in these trajectories are plotted in the Supplementary Fig. S7 of the paper. Force field: Amber99sb.

pull_MD_amber.zip: MD simulation where Na+ and K+ were pulled through the selectivity filter. Force field: Amber99sb.

us_K_amber.zip: Umbrella Sampling for a potassium ion. Force field: Amber99sb.

free_MD_charmm.zip: free MD at Vtm = −100 mV. Results of this Charmm modeling are reported in the Supplementary Fig. S7 of the paper. Force field: Charmm36m.