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Python (helper) files

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 .xvg file. 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 .log files of the simulations.