Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60461373%3A22330%2F19%3A43918068" target="_blank" >RIV/60461373:22330/19:43918068 - isvavai.cz</a>
Result on the web
<a href="https://www.frontiersin.org/articles/10.3389/fmolb.2019.00025/full" target="_blank" >https://www.frontiersin.org/articles/10.3389/fmolb.2019.00025/full</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.3389/fmolb.2019.00025" target="_blank" >10.3389/fmolb.2019.00025</a>

Result language
angličtina
Original language name
Anncolvar: Approximation of Complex Collective Variables by Artificial Neural Networks for Analysis and Biasing of Molecular Simulations
Original language description
The state of a molecular system can be described in terms of collective variables. These low-dimensional descriptors of molecular structure can be used to monitor the state of the simulation, to calculate free energy profiles or to accelerate rare events by a bias potential or a bias force. Frequent calculation of some complex collective variables may slow down the simulation or analysis of trajectories. Moreover, many collective variables cannot be explicitly calculated for newly sampled structures. In order to address this problem, we developed a new package called anncolvar. This package makes it possible to build and train an artificial neural network model that approximates a collective variable. It can be used to generate an input for the open-source enhanced sampling simulation PLUMED package, so the collective variable can be monitored and biased by methods available in this program. The computational efficiency and the accuracy of anncolvar are demonstrated on selected molecular systems (cyclooctane derivative, Trp-cage miniprotein) and selected collective variables (Isomap, molecular surface area).
Czech name
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Czech description
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Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry

Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)<br>S - Specificky vyzkum na vysokych skolach

Publication year
2019
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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