The python directory contains Python files that aid in the simulation pipeline.
These are called by the scripts.
mean_frame_xvg_2_col.py: A script to calculate the mean of a subset of frames from a 2 column.xvgfile. This is used to calculate the average density from an NPT simulation and pick a frame that is closest to the average density for future NVT simulations.setup_umbrella.sh: A modified version of a file Justin Lemkul provided in a tutorial. This will generate the input files for an umbrella sampling simulation. The input is a "pull" file where the collective variable has been varied using a steered-MD approach. The script then generates N independent windows (simulations) for the range of the collective variable.