Output

Outputs of the reaction process are as follows:

• Folder "min" contains energy minimization files of each loop.
• Folder "md" contains MD simulation files of each loop.
• Folder "itp" contains itp files of the system in each loop.
• File "conversion.xvg" contains the trend of conversion of the reaction for each reactive bead.
• Files "product.itp" and "topol.top" are the topology files of the system for the last loop.
• The txt files named to your reactive beads, contain the indices of beads that do not react until the current loop.
• File "XL.txt" contains the beads that are located at a specified distance, and so can react.
• File "XL_noprob.txt" contains the "XL.txt" information before applying the probability of the reaction between beads.
• Folder "loops" contain the reactions that take place between bead pairs in each loop. The file "all_loops" contains all the reactions so far.
• Files "undefined_angles.txt" and "undefined_dihedrals" contain the new angles and dihedrals that are formed due to the reactions but the user does not define their parameters in corresponding input files and so they are not added to the topology file.