Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague
Molecular metadynamics is a method of accelerated exploration of free energy surface (i.e. possible shapes - conformations) of large molecules, typically proteins, by adding artificial "bias" energy to the simulation. However, the principal advantages of metadynamics are jeopardized by the computational complexity of the bias calculation.
We developed an approximative method which speeds up the bias calculation dramatically while not affecting the overall precision of the method.
The method was implemented in Plumed and Gromacs software, it will be included in the 2017 release of Plumed.
In 2015–2016, the work was supported by GACR project "Enhanced Sampling Simulations for Complex Systems", proj. no. 15-17269S.
This work was supported by the projects OP RI CERIT Scientific Cloud LM2015085; GACR: Enhanced Sampling Simulations for Complex Systems 15-17269S.
You are running an old browser version which is not fully supported information system anymore. Some applications might not display correctly, some functions might not work as expected or might not work at all.