The analysis_files folder contains scripts used for the analysis of trajectories

The fcgriiia_adf4_simulations;
    fcgriiia_adg3_simulations;
    fcgriiib-na2_adf4_simulations; and
    fcgriiib-na2_adg3_simulations folders each contain three simulations files (.x) along with a topology file for watching of the simulations (.top). Each .x file contains the positions and velocities of each atom in the simulation, which is recorded at a 1ps time interval over the course of the simulation timeframe.

The input_files folder contains files that can be used for repeating our simulations. The conditions used for the simulations can be found in these input files. For further guidance please see the Amber14 manual (http://ambermd.org/doc12/Amber14.pdf)


Files types:

.x - simulation file
.top - topology file for viewing, running and analysing simulation trajectories
.crd - coordinate files used for starting simulations
.in - input files specifying the conditions used for each part of the simulation, is read by .sh files
.sh - execution files for submission of simulations jobs to a supercomputer. Contains instructions for the supercomputer on how to run simulations and where to find input files.
no file extension - ptrajscript file for analysis of simulations