We used the CGenff tool () to generate force fields for caffeine, as demonstrated in Figure . The input molecule for CGenff can be in mol2, sdf, or pdb formats. We obtained the caffeine sdf file from PubChem () and uploaded it to the CGenff tool. The output file contains the information for caffeine structures and parameters. We split them into Caffeine.str and Caffeine.prm, which is the convention for the VMD and NAMD program. This flowchart applies to many small organic molecules.