Molecular Dynamics with Helical Periodic Boundary Conditions

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11310%2F14%3A10287511" target="_blank" >RIV/00216208:11310/14:10287511 - isvavai.cz</a>

Alternative codes found

RIV/61388963:_____/14:00431486

Result on the web

<a href="http://dx.doi.org/10.1002/jcc.23653" target="_blank" >http://dx.doi.org/10.1002/jcc.23653</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1002/jcc.23653" target="_blank" >10.1002/jcc.23653</a>

Result language

angličtina

Original language name

Molecular Dynamics with Helical Periodic Boundary Conditions

Original language description

Helical symmetry is often encountered in nature and thus also in molecular dynamics (MD) simulations. In many cases, an approximation based on infinite helical periodicity can save a significant amount of computer time. However, standard simulations withthe usual periodic boundary conditions (PBC) are not easily compatible with it. In the present study, we propose and investigate an algorithm comprising infinitely propagated helicity, which is compatible with commonly used MD software. The helical twist is introduced as a parametric geometry constraint, and the translational PBC are modified to allow for the helical symmetry via a transitional solvent volume. The algorithm including a parallel code was implemented within the Tinker software. The viability of the helical periodic boundary conditions (HPBC) was verified in test simulations including alpha-helical and polyproline II like peptide structures. For an insulin-based model, the HPBC dynamics made it possible to simulate a fibr

Czech name

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Czech description

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Type

J_x - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)

CEP classification

CF - Physical chemistry and theoretical chemistry

OECD FORD branch

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Project

Result was created during the realization of more than one project. More information in the Projects tab.

Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2014

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

Journal of Computational Chemistry

ISSN

0192-8651

e-ISSN

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Volume of the periodical

35

Issue of the periodical within the volume

21

Country of publishing house

US - UNITED STATES

Number of pages

8

Pages from-to

1552-1559

UT code for WoS article

000339958200003

EID of the result in the Scopus database

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