Dynamic-radius Species-conserving Genetic Algorithm for de novo Protein Folding Instructions Dynamic-radius Species-conserving Genetic Algorithm for de novo Protein Folding is a Java application written in Java version 1.7, but it should run on other versions of Java. There are 10 command line parameters that should be set: # position 1 - population size # position 2 - number of generations # position 3 - mutation rate (decimal) # position 4 - initial radius (decimal) # position 5 - radius delta (decimal) # position 6 - reevaluation loop count # position 7 - convergence limit # position 8 - protein # position 9 - output file location # position 10 - log status 0 few logs; 1 more logs; 2 most logs An output file will be placed in the file location for position 9. Here is an example for running the application: java -jar /Users/mbrown15/NetBeansProjects/DSGAProteinFolding/dist/DSGAProteinFoldingKG.jar 1000 2000 0.03 8.0 -1.0 500 4 PPHPPHHPPHHPPPPPHHHHHHHHHHPPPPPPHHPPHHPPHPPHHHHH //Users//mbrown15//Documents//genetic-algorithm-files// 1 This method allows multiple runs to be placed in a batch file. The class called TestAllCombinationsSample will generate a file for Figure 2. The file GAProteinFoldingDD has the code for the traditional Genetic Algorithm.