Cluster-fusion-fission-analyzer

Tutorial

1. Prepare a trajectory, put the .gro or .xyz ... files in /conf.
2. Run clustering(), read the files and cluster data will be placed in /Index.
3. Set the value of max cluster size from last step,set the size of box, set the number of frames, run splitTraceBack() and rate coefficients alpha and beta will be placed in /rate.
4. Run splitAverageRate(), compute the average rate matrix.
5. Edit the file name in NeoVisual.py, and draw the pcolor figure.

About example conformation files

Because the size of full trajactory file is large (over 15 GB), only a small example conf file is provided in this repo. The parameters should be altered before computing on this example file.