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. 2021 Jun 26;13(7):966. doi: 10.3390/pharmaceutics13070966

Figure 2.

Figure 2

Figure 2

(a) Free energy surfaces (in kcal/mol) for the aggregation of AH-798 forming a disulfide bridge in terms of the radius of gyration (Rgyr) and the root mean square deviation (RMSD). The darker region represents the lower energy of the structure, and the conformation with the lowest energy is indicated with an arrow. (b) Potential energy (black), kinetic energy (red) and total energy (green) fluctuation of the system during the production molecular dynamics simulation within 100 ns; (c) Lennard-Jones Short Range potential (black) and Coulomb short-range force (red) fluctuation of the system during the production molecular dynamics simulation within 100 ns. (d) Root mean square fluctuation (RMSF) of the Cα in the structure of AH-798 (indicated with black lines) and the carbon backbone of the structure (indicated with red lines). (e) The root mean square deviation (RMSD) values of the Cα in the structure of AH-798 during the production molecular dynamics simulation within 100 ns. (f) Radius of gyration (Rg) of the whole conformation during the molecular dynamics simulation within 100 ns.