On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers

Abstract

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 NH2-(RADA)4-COOH in the β-conformation at two temperatures (300K and 320K). 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 β-structure of the dimer at 300K, while ff96 not only ensures the highest stability of the initial b-peptide conformation at higher temperatures, but also enhances the retention of antiparallel β-conformation, which determines the ability of NH2-(RADA)4-COOH peptides to self-organization.