This repository records the files and scripts for setting up umbrella samplings of full ribosome structures with the following scenarios:
- full ribosome using stand smog model
- full ribosome using smog_ion model without the presence of ions (only assign partial charges to atoms)
- full ribosome using smog_ion model with the presence of ions
There are two umbrella coordinates in the system: UC1: center of geometry (cog) of A-elbow ~ cog of P-elbow UC2: cog of A-elbow ~ cog of protein L14
All structure files and topology files are in "structure" folder. Scripts for submitting simulations on discussion are in "scripts" folder.