Reducing the number of mean-square deviation calculations with floating close structure in metadynamics

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216224%3A14610%2F17%3A00094853" target="_blank" >RIV/00216224:14610/17:00094853 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60461373:22330/17:43913706

Výsledek na webu

<a href="http://aip.scitation.org/doi/abs/10.1063/1.4978296" target="_blank" >http://aip.scitation.org/doi/abs/10.1063/1.4978296</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1063/1.4978296" target="_blank" >10.1063/1.4978296</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Reducing the number of mean-square deviation calculations with floating close structure in metadynamics

Popis výsledku v původním jazyce

Metadynamics is an important collective-coordinate-based enhanced sampling simulation method. Its performance depends significantly on the capability of collective coordinates to describe the studied molecular processes. Collective coordinates based on comparison with reference landmark structures can be used to enhance sampling in highly complex systems; however, they may slow down simulations due to high number of structure-structure distance (e.g., mean-square deviation) calculations. Here we introduce an approximation of root-mean-square or mean-square deviation that significantly reduces numbers of computationally expensive operations. We evaluate its accuracy and theoretical performance gain with metadynamics simulations on two molecular systems. Published by AIP Publishing.

Název v anglickém jazyce

Reducing the number of mean-square deviation calculations with floating close structure in metadynamics

Popis výsledku anglicky

Metadynamics is an important collective-coordinate-based enhanced sampling simulation method. Its performance depends significantly on the capability of collective coordinates to describe the studied molecular processes. Collective coordinates based on comparison with reference landmark structures can be used to enhance sampling in highly complex systems; however, they may slow down simulations due to high number of structure-structure distance (e.g., mean-square deviation) calculations. Here we introduce an approximation of root-mean-square or mean-square deviation that significantly reduces numbers of computationally expensive operations. We evaluate its accuracy and theoretical performance gain with metadynamics simulations on two molecular systems. Published by AIP Publishing.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10201 - Computer sciences, information science, bioinformathics (hardware development to be 2.2, social aspect to be 5.8)

Projekt

Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.

Návaznosti

P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)

Rok uplatnění

2017

Kód důvěrnosti údajů

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

Název periodika

Journal of Chemical Physics

ISSN

0021-9606

e-ISSN

—

Svazek periodika

146

Číslo periodika v rámci svazku

11

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

8

Strana od-do

„115101:1“-„115101:8“

Kód UT WoS článku

000397313600032

EID výsledku v databázi Scopus

2-s2.0-85015630113