Anncolvar: Approximation of complex collective variables by artificial neural networks for analysis and biasing of molecular simulations

Dalibor Trapl, Izabela Horvacanin, Vaclav Mareska, Furkan Ozcelik, Gozde Unal, Vojtech Spiwok*

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20 Atıf (Scopus)

Özet

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).

Orijinal dilİngilizce
Makale numarası25
DergiFrontiers in Molecular Biosciences
Hacim6
Basın numarasıAPR
DOI'lar
Yayın durumuYayınlandı - 2019

Bibliyografik not

Publisher Copyright:
© 2019 Trapl, Horvacanin, Mareska, Ozcelik, Unal and Spiwok.

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