Perturbation Scripts

Here are the scripts that allowed us to carry out the mutations between ions in the various environments. These are sample ones that are representative of the rest of the scripts used in the research. Multiple runs were carried out for each system by changing the initial velocities by using different ISEED values during the dynamics runs.

Mutations in protein (longer running times)

  • Ca++ to Mg++
  • Mg++ to Ca++
  • Ca++ to Ba++
  • Ba++ to Ca++

    • Mutations in other systems (shorter running times)

  • Ca++ to Mg++ in acetate
  • Mg++ to Ca++ in acetate
  • Ca++ to Ba++ in acetate
  • Ba++ to Ca++ in acetate

    • Sample PUNIT files that determine rate of change of Lambda

  • Linear Change in Lambda
  • End Weighting - Incremental Change in Lambda greatest in beginning of run, allowing more steps of dynamics at the end, for larger to smaller radius mutations.
  • Front Weighting - Incremental Change in Lambda greatest in end of run, allowing more steps of dynamics at the beginning, for smaller to larger radius mutations.