An evaluation of non-periodic boundary condition models in molecular dynamics simulations using prion octapeptides as probes
2006 (English)In: Journal of Molecular Structure: THEOCHEM, ISSN 0166-1280, Vol. 760, no 1-3, 91-98 p.Article in journal (Refereed) Published
Molecular dynamics simulations have been performed under periodic boundary conditions and using four non-periodic solvation models. The biomolecular probe in these simulations was a single repeat of the copper-binding octapeptide in the human prion protein, PHGGGWGQ. Although the alternative non-periodic solvation models enable a reduction in computational time, the dynamical disadvantages are considerable when using any of these four non-periodic models. For simulations of systems similar to the test system, periodic boundary conditions are a better alternative than any of the four local models.
Place, publisher, year, edition, pages
2006. Vol. 760, no 1-3, 91-98 p.
Molecular dynamics; Non-periodic boundary conditions; Prion protein; Solvation model
IdentifiersURN: urn:nbn:se:kth:diva-7295DOI: 10.1016/j.theochem.2005.11.027ISI: 000236566300011ScopusID: 2-s2.0-33644817645OAI: oai:DiVA.org:kth-7295DiVA: diva2:12259
QC 201008162007-06-042007-06-042010-08-16Bibliographically approved