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.probability_exchange.py: A script to calculate the probability of exchange between HREMD replicas from the.logfiles of the simulations.