Uncertainties of Predictions from Temperature Replica Exchange Simulations

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F24%3A43928911" target="_blank" >RIV/60461373:22330/24:43928911 - isvavai.cz</a>

Nalezeny alternativní kódy

RIV/60461373:22340/24:43928911 RIV/00216208:11320/24:10490148

Výsledek na webu

<a href="https://doi.org/10.1063/5.0204992" target="_blank" >https://doi.org/10.1063/5.0204992</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1063/5.0204992" target="_blank" >10.1063/5.0204992</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Uncertainties of Predictions from Temperature Replica Exchange Simulations

Popis výsledku v původním jazyce

Parallel tempering molecular dynamics simulation, also known as temperature replica exchange simulation, is a popular enhanced sampling method used to study biomolecular systems. This method makes it possible to calculate the free energy differences between states of the system for a series of temperatures. We developed a method to easily calculate the errors (standard errors or confidence intervals) of these predictions using a modified version of our recently introduced JumpCount method. The number of transitions between states (e.g., protein folding events) is counted for each temperature. This number of transitions, together with the temperature, fully determines the value of the standard error or the confidence interval of the free energy difference. We also address the issue of convergence in the situation where all replicas start from one state by developing an estimator of the equilibrium constant from simulations that are not fully equilibrated. The prerequisite of the method is the Markovianity of the process studied.

Název v anglickém jazyce

Uncertainties of Predictions from Temperature Replica Exchange Simulations

Popis výsledku anglicky

Parallel tempering molecular dynamics simulation, also known as temperature replica exchange simulation, is a popular enhanced sampling method used to study biomolecular systems. This method makes it possible to calculate the free energy differences between states of the system for a series of temperatures. We developed a method to easily calculate the errors (standard errors or confidence intervals) of these predictions using a modified version of our recently introduced JumpCount method. The number of transitions between states (e.g., protein folding events) is counted for each temperature. This number of transitions, together with the temperature, fully determines the value of the standard error or the confidence interval of the free energy difference. We also address the issue of convergence in the situation where all replicas start from one state by developing an estimator of the equilibrium constant from simulations that are not fully equilibrated. The prerequisite of the method is the Markovianity of the process studied.

Druh

J_imp - Článek v periodiku v databázi Web of Science

CEP obor

—

OECD FORD obor

10608 - Biochemistry and molecular biology

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

2024

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

1089-7690

Svazek periodika

160

Číslo periodika v rámci svazku

18

Stát vydavatele periodika

US - Spojené státy americké

Počet stran výsledku

12

Strana od-do

"184116-i"-"184116-xii"

Kód UT WoS článku

001222371200009

EID výsledku v databázi Scopus

2-s2.0-85192712594