Use a dielectric screening function for electrostatics
Assume that mdcrd always has box information
Add command line flags to force reading or ignoring mdcrd box info
Add script to render rescorrel matrices to PNG
Report number of residues in solute on coulomb startup
Revise default dielectric constant to 4, to (hopefully) more accurately represent protein
Make dielectric constant a command line optionand make its code less verbose
Use C99 variable scoping for great clarity
Need string.h for strtok
Don't save pairs correlation matrix or unpruned pairs list (which is intermediate data)
Whoops, we actually do want to write out correl.txt
Allow energy and correlation cutoffs to be specified as command-line arguments
Allow specifying a subset of mdcrd frames to process
Make sure user actually specified FramesToProcess before complaining they specified it wrong
Fix matrix parsing