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5 papers
PLUMED: a portable plugin for free-energy calculations with molecular dynamics
M. Bonomi, D. Branduardi, G. Bussi +8
Here we present a program aimed at free-energy calculations in molecular systems. It consists of a series of routines that can be interfaced with the most popular classical molecul…
Metadynamic sampling of the free energy landscapes of proteins coupled with a Monte Carlo algorithm
F. Marini, C. Camilloni, D. Provasi +2
Metadynamics is a powerful computational tool to obtain the free energy landscape of complex systems. The Monte Carlo algorithm has proven useful to calculate thermodynamic quantit…
Exploring the Protein G Helix Free Energy Surface by Solute Tempering Metadynamics
C. Camilloni, D. Provasi, G. Tiana +1
The free-energy landscape of the alpha-helix of protein G is studied by means of metadynamics coupled with a solute tempering algorithm. Metadynamics allows to overcome large energ…
Design of HIV-1-PR inhibitors which do not create resistance: blocking the folding of single monomers
R. A. Broglia, G. Tiana, L. Sutto +2
One of the main problems of drug design is that of optimizing the drug--target interaction. In the case in which the target is a viral protein displaying a high mutation rate, a se…
Room Temperature Organic Superconductor?
N. Breda, R. A. Broglia, G. Colo` +3
The electron--phonon coupling in fullerene C28 has been calculated from first principles. The value of the associated coupling constant lambda/N(0) is found to be a factor three la…