Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

Kód výsledku v IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F16%3A43899851" target="_blank" >RIV/60461373:22330/16:43899851 - isvavai.cz</a>

Výsledek na webu

<a href="http://www.sciencedirect.com/science/article/pii/S0010465515003367" target="_blank" >http://www.sciencedirect.com/science/article/pii/S0010465515003367</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1016/j.cpc.2015.08.037" target="_blank" >10.1016/j.cpc.2015.08.037</a>

Jazyk výsledku

angličtina

Název v původním jazyce

Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

Popis výsledku v původním jazyce

Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

Název v anglickém jazyce

Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

Popis výsledku anglicky

Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

Druh

J_x - Nezařazeno - Článek v odborném periodiku (Jimp, Jsc a Jost)

CEP obor

CE - Biochemie

OECD FORD obor

—

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)<br>S - Specificky vyzkum na vysokych skolach

Rok uplatnění

2016

Kód důvěrnosti údajů

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

Název periodika

Computer Physics Communications

ISSN

0010-4655

e-ISSN

—

Svazek periodika

198

Číslo periodika v rámci svazku

leden 2016

Stát vydavatele periodika

NL - Nizozemsko

Počet stran výsledku

8

Strana od-do

222-229

Kód UT WoS článku

000365370800020

EID výsledku v databázi Scopus

2-s2.0-84947018921