Metadynamics combined with auxiliary density functional and density functional tight-binding methods: alanine dipeptide as a case study

NMR characterization of dilauroyl phosphatidylcholine in adsorbed monolayers at fluid interfaces studied by multiscale computations

(2016) Yana Tsoneva et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

(2015) Alejandro Gil-Ley et al.   Journal of Chemical Theory and Computation

Cationic Methylene–Pyrene Isomers and Isomerization Pathways: Finite Temperature Theoretical Studies

(2015) Mathias Rapacioli et al.   JOURNAL OF PHYSICAL CHEMISTRY A

Phase changes of the water hexamer and octamer in the gas phase and adsorbed on polycyclic aromatic hydrocarbons

(2015) Luiz Fernando L. Oliveira et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Umbrella sampling of proton transfer in a creatine–water system

(2014) Olga Ivchenko et al.   CHEMICAL PHYSICS LETTERS

Aqueous solutions: state of the art in ab initio molecular dynamics

(2014) A. A. Hassanali et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A-MATHEMATICAL PHYSICAL AND ENGINEERING SCIENCES

Variational Approach to Enhanced Sampling and Free Energy Calculations

(2014) Omar Valsson et al.   PHYSICAL REVIEW LETTERS

13C NMR chemical shift calculations of charged surfactants in water — A combined density functional theory (DFT) and molecular dynamics (MD) methodological study

(2013) T. Mineva et al.   CANADIAN JOURNAL OF CHEMISTRY

PLUMED 2: New feathers for an old bird

(2013) Gareth A. Tribello et al.   COMPUTER PHYSICS COMMUNICATIONS

Temperature dependence of the molecular conformations of dilauroyl phosphatidylcholine: A density functional study

(2012) Tzonka Mineva et al.   INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY

Improved Statistical Sampling and Accuracy with Accelerated Molecular Dynamics on Rotatable Torsions

(2012) Urmi Doshi et al.   Journal of Chemical Theory and Computation

Parametrization and Benchmark of DFTB3 for Organic Molecules

(2012) Michael Gaus et al.   Journal of Chemical Theory and Computation

Contribution of high-energy conformations to NMR chemical shifts, a DFT-BOMD study

(2012) A. Goursot et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Density-functional tight binding-an approximate density-functional theory method

(2012) Gotthard Seifert et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Comparison of Free Energy Surfaces Calculations from Ab Initio Molecular Dynamic Simulations at the Example of Two Transition Metal Catalyzed Reactions

(2011) Marc Brüssel et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)

(2011) Michael Gaus et al.   Journal of Chemical Theory and Computation

14N: A Sensitive NMR Probe for the Study of Surfactant–Oxide Interfaces

(2011) Tzonka Mineva et al.   Journal of Physical Chemistry C

deMon2k

(2011) Gerald Geudtner et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

Metadynamics

(2011) Alessandro Barducci et al.   Wiley Interdisciplinary Reviews-Computational Molecular Science

The Self-Consistent Charge Density Functional Tight Binding Method Applied to Liquid Water and the Hydrated Excess Proton: Benchmark Simulations

(2010) C. Mark Maupin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Enhanced Sampling in the Well-Tempered Ensemble

(2010) M. Bonomi et al.   PHYSICAL REVIEW LETTERS

PLUMED: A portable plugin for free-energy calculations with molecular dynamics

(2009) Massimiliano Bonomi et al.   COMPUTER PHYSICS COMMUNICATIONS

Does Water Relay Play an Important Role in Phosphoryl Transfer Reactions? Insights from Theoretical Study of a Model Reaction in Water andtert-Butanol

(2009) Yang Yang et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Density-functional based tight-binding: an approximate DFT method

(2009) Augusto F. Oliveira et al.   JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY

Proton Transfer in Carbonic Anhydrase Is Controlled by Electrostatics Rather than the Orientation of the Acceptor†

(2008) Demian Riccardi et al.   BIOCHEMISTRY

Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide

(2008) Birgit Strodel et al.   CHEMICAL PHYSICS LETTERS

Lipid Thermodynamics: Melting is Molecular

(2008) Sailaja Krishnamurty et al.   CHEMPHYSCHEM

Extensive Conformational Transitions Are Required to Turn On ATP Hydrolysis in Myosin

(2008) Yang Yang et al.   JOURNAL OF MOLECULAR BIOLOGY

Molecular Dynamics Prediction of the Mechanism of Ester Hydrolysis in Water

(2008) Hakan Gunaydin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Well-Tempered Metadynamics: A Smoothly Converging and Tunable Free-Energy Method

(2008) Alessandro Barducci et al.   PHYSICAL REVIEW LETTERS

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science

(2008) Alessandro Laio et al.   REPORTS ON PROGRESS IN PHYSICS