Geodesic
On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers
Matematičeskaâ biologiâ i bioinformatika, Tome 13 (2018), pp. t29-t38.

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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. 
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     author = {A. V. Danilkovich and D. A. Tikhonov and E. V. Sobolev and T. E. Shadrina and I. P. Udovichenko},
     title = {On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers},
     journal = {Matemati\v{c}eska\^a biologi\^a i bioinformatika},
     pages = {t29--t38},
     publisher = {mathdoc},
     volume = {13},
     year = {2018},
     language = {en},
     url = {http://geodesic.mathdoc.fr/item/MBB_2018_13_a2/}
}
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A. V. Danilkovich; D. A. Tikhonov; E. V. Sobolev; T. E. Shadrina; I. P. Udovichenko. On the choice of force fields for studying the molecular dynamics of ion peptides and their dimers. Matematičeskaâ biologiâ i bioinformatika, Tome 13 (2018), pp. t29-t38. http://geodesic.mathdoc.fr/item/MBB_2018_13_a2/

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