"433013" . . "Metadynamika v esenci\u00E1ln\u00EDch sou\u0159adnic\u00EDch: modelov\u00E1n\u00ED voln\u00FDch energi\u00ED konforma\u010Dn\u00EDch zm\u011Bn"@cs . . . . "Metadynamics in essential coordinates: Free energy simulation of conformational changes" . "RIV/60461373:22330/07:00019130!RIV08-AV0-22330___" . . "[3502DD851D12]" . . . "Metadynamics in essential coordinates: Free energy simulation of conformational changes"@en . "JOURNAL OF PHYSICAL CHEMISTRY B" . . "metadynamics; free energy surface; essential dynamics"@en . . "RIV/60461373:22330/07:00019130" . "Lipovov\u00E1, Petra" . "3"^^ . "111" . "Metadynamics in essential coordinates: Free energy simulation of conformational changes" . "3"^^ . . . . "3073-3076" . "Byla provedena metadynamika v esenci\u00E1ln\u00EDch sou\u017Eadnic\u00EDch"@cs . "We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surf"@en . . . "Metadynamika v esenci\u00E1ln\u00EDch sou\u0159adnic\u00EDch: modelov\u00E1n\u00ED voln\u00FDch energi\u00ED konforma\u010Dn\u00EDch zm\u011Bn"@cs . . . "12" . "We propose an approach that combines an extraction of collective motions of a molecular system with a sampling of its free energy surface. A recently introduced method of metadynamics allows exploration of the free energy surface of a molecular system by means of coarse-grained dynamics with flooding of free energy minima. This free energy surface is defined as a function of a set of collective variables (e.g., interatomic distances, angles, torsions, and others). In this study, essential coordinates determined by essential dynamics (principle component analysis) were used as collective variables in metadynamics. First, dynamics of the model system (explicitly solvated alanine dipeptide, Ace-Ala-Nme) was simulated by a classical molecular dynamics simulation. The trajectory (1 ns) was then analyzed by essential dynamics to obtain essential coordinates. The free energy surface as a function of the first and second essential coordinates was then explored by metadynamics. The resulting free energy surf" . "Metadynamics in essential coordinates: Free energy simulation of conformational changes"@en . "P(KJB500500512), Z(MSM6046137305)" . . "US - Spojen\u00E9 st\u00E1ty americk\u00E9" . "Kr\u00E1lov\u00E1, Blanka" . "4"^^ . . "22330" . "1520-6106" . . "Spiwok, Vojt\u011Bch" .