Considering usage of different force-fields for molecular dynamic studies of the ionic peptides and their dimers

The paper presents comparative data on the impact of force-fields AMBER (ff03, ff99SB, and ff96) on the results of molecular dynamics experiments with dimeric molecules formed by ion-peptide $\mathrm{NH_2\text-(RADA)_4\text-COOH}$ in the $\beta$-conformation at two temperatures (300 K and 320 K). It is shown that an MD simulation in explicit water environment is the most informative approach. The use of different force-fields has a significant influence on the stability of the initial molecular conformation of the peptide over time. Finally, the simulation in ff99SB environment provides significant stability of antiparallel $\beta$-structure of the dimer at 300 K, while ff96 not only ensures the highest stability of the initial b-peptide conformation at higher temperatures, but also enhances the retention of antiparallel $\beta$-conformation, which determines the ability of $\mathrm{NH_2\text-(RADA)_4\text-COOH}$ peptides to self-organization.