BrainChildren Chemistry
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BrainChildren Chemistry
Atomic
Atomic and Molecular Systems
Molecular Dynamics
Parents
Atomic and Molecular Systems
Atomic Scale
Biology
Biophysics
Biophysics Simulations
Classical Systems
Computational Biology
Computational Catalysis
Computational chemistry, Computational efficiency
Computational Methods
Computational methods and simulations, Computational modeling and simulations
Computational Modeling
Computational Models
Computational Simulations
Computational Studies
Computational Techniques
Computational tools (chemistry)
Dynamic
Dynamics
Equilibrium and Kinetics
Importance and applications
In Silico Modeling
loose ion pair
Model Building
Modeling Techniques
Modeling Transient Species
Molecular
Molecular Modeling
Molecular Simulations
Neutron Spectroscopy in Biological and Chemical Systems
Nuclear Magnetic Resonance (NMR)
Numerical Methods
Photodissociation
Predictive Models
Property prediction
Protein Folding
Protein Structures
Quantum Chemistry
Quantum Mechanical Calculations
Reaction Modelling
Reaction Pathway Exploration
Sampling Techniques
Scientific Computing
Simulation and Modeling
Simulation Software
Simulation Techniques
Theoretical Chemistry
Theoretical Framework, steric-approach control
Theoretical Models
Theoretical Studies, Carbonyl Carbon
Children
133 Endogenous lipid activated G protein-coupled receptors: emerging structural features from crystallography and molecular dynamics simulations
138 Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints
1406. Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation
1414. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes
144 Molecular dynamics of rhodopsin and free opsin: computer simulation
146 Molecular dynamics simulation of dark-adapted rhodopsin and free opsin
147 Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin
239. Endogenous lipid activated G protein-coupled receptors: Emerging structural features from crystallography and molecular dynamics simulations
326. QM/MM molecular dynamics simulations provide insight into the photoisomerization mechanism of retinal in rhodopsin and an artificial molecular switch
339. Light Activation of Rhodopsin: Insights from Molecular Dynamics Simulations Guided by Solid-State NMR Distance Restraints
37 Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation
388. Mechanism of signal propagation upon retinal isomerization: insights from molecular dynamics simulations of rhodopsin restrained by normal modes
438. Molecular dynamics of rhodopsin and free opsin: computer simulation
45 Rhodopsin Activation Studied by Microsecond-Time Scale Molecular Dynamics Simulations
467. Molecular dynamics simulation of dark-adapted rhodopsin and free opsin
470. Visual pigment rhodopsin: a computer simulation of the molecular dynamics of 11-cis-retinal chromophore and amino-acid residues in the chromophore centre
49 Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin
a) Classical Molecular Dynamics
ab initio MD
Ab Initio Molecular Dynamics
Ab Initio Molecular Dynamics (AIMD)
Accelerated Molecular Dynamics
Activation enthalpy in, molecular dynamics
Adiabatic and Non-Adiabatic Transitions
Adiabatic Elimination
Adiabatic Potential Energy Surfaces
Algorithms
Allosteric Transition
Analysis Techniques in Classical Molecular Dynamics
Anharmonic Potential Models
Applications in Drug Design
Applications in Protein Folding
Applications in Solvent Effects
Applications of Classical Molecular Dynamics
Applications of ultrafast electron transfer in molecular dynamics
Binding Site Prediction
Biochemistry (2005), 44(38), 12667-80, 147 Molecular dynamics simulations of retinal in rhodopsin: from the dark-adapted state towards lumirhodopsin
Biological systems and molecular dynamics
Biomolecular Simulations
Biomolecular Structure and Dynamics
Biophysical journal (1981), 34(3), 517-34, 1757. Molecular dynamics of trans-cis isomerization in bathorhodopsin
Car-Parrinello Molecular Dynamics (CPMD)
Catalyst-Substrate Interactions
CHARMM force field in molecular dynamics simulations
Chemical Dynamics and Molecular Reactions
Chemistry and physics of lipids (2013), 16946-56, 133 Endogenous lipid activated G protein-coupled receptors: emerging structural features from crystallography and molecular dynamics simulations
Classical MD
Classical Molecular Dynamics
Classical molecular dynamics (MD)
Coarse-Grained Molecular Dynamics
Coherent control and manipulation of molecular dynamics
Conformational Changes
Definition and Simulation
Dissociation Channels
Distance Geometry and Molecular Dynamics
Drug Discovery
Eclipsing Strain and Molecular Dynamics Simulations
Elasticity and molecular dynamics
Electron transfer processes
Energy Calculations
Energy Conservation
Energy Distribution
Energy Minimization
Enhanced sampling techniques
Ensemble Methods in Classical Molecular Dynamics
Ensemble Types
Excited-state dynamics in biomolecular interactions
Excited-state dynamics in molecular aggregates
Experimental Techniques
Exploration of quantum control of molecular dynamics
Fluorescence spectroscopy in studying pseudo-unimolecular dynamics
Force Fields
Force Fields in Classical Molecular Dynamics
Formation of Loose Ion Pairs
Free Energy Calculations
Frontier molecular orbital theory vs. molecular dynamics
Hartree-Fock for Molecular Dynamics
How to Create Simple Molecular Dynamics Simulations in Chimera
Hückel Molecular Dynamics (HMD)
Identifying rate-controlling steps
Importance in studying molecular interactions and dynamics
Insights into molecular dynamics
Integrating molecular dynamics and quantum chemistry
Interatomic Potentials
Interface with Molecular Dynamics (MD) Software
Introduction to Molecular Dynamics
Journal of molecular biology (2007), 372(1), 50-66, 1429. Structural analysis and dynamics of retinal chromophore in dark and meta I states of rhodopsin from 2H NMR of aligned membranes
Journal of molecular biology (2010), 396(3), 510-27, 138 Light activation of rhodopsin: insights from molecular dynamics simulations guided by solid-state NMR distance restraints
Langevin Dynamics
Lewis structures and molecular dynamics simulations
Mapping Molecular Dynamics
Methods
Methods in Molecular Biology (New York, NY, United States) (2012), 914(Membrane Protein Structure and Dynamics), 25-45.
Modeling Heat Transfer
Molecular Docking and Molecular Dynamics
Molecular dynamics (MD)
Molecular dynamics (MD) simulations
Molecular Dynamics Algorithms
Molecular Dynamics and Berry Phase
Molecular Dynamics and Collisions
Molecular Dynamics Aticles
Molecular dynamics method
Molecular Dynamics Methods
Molecular dynamics of hemoglobin
Molecular Dynamics of Nanobiostructures (2012), 25-4
Molecular dynamics simulation
Molecular Dynamics Simulation Articles
Molecular Dynamics Simulation Software
Molecular Dynamics Simulation Videos
Molecular Dynamics Simulations
Molecular Dynamics Simulations and Bond Angles
Molecular dynamics simulations and calculations
Molecular dynamics simulations and charge density
Molecular dynamics simulations and energy calculations
Molecular dynamics simulations and microscopic reversibility
Molecular dynamics simulations of biomolecules
Molecular dynamics simulations of contact ion pairs
Molecular Dynamics Simulations of Degenerate Rearrangement
Molecular dynamics simulations of deprotonation
Molecular Dynamics Simulations of Electron Attachment
Molecular dynamics simulations of pseudo-unimolecular interactions
Molecular dynamics simulations of small molecules
Molecular dynamics simulations of vaporization processes
Molecular dynamics studies
Molecular Dynamics Videos
Molecular Dynamics with Biasing Potentials
Monte Carlo Simulations
Newtonian Dynamics
Non-adiabatic Dynamics
Non-Adiabatic Molecular Dynamics
Nonadiabatic Transitions
Nuclear Motion
Nuclear Motion in Molecular Dynamics
Polymer Behavior
Potential Energy Surface
Potential Energy Surfaces
Principle
Principles
Principles of Classical Molecular Dynamics
PyMOL and molecular dynamics simulations
Quantum chemical calculations, Quantum chemistry calculations
Quantum Effects on Molecular Motion
Quantum MD
Quantum Mechanics
Quantum Molecular Dynamics
Quantum Molecular Dynamics (QMD) Simulations
Quantum molecular dynamics simulations of the effect of secondary modes on the photoisomerization of a retinal chromophore model
Reaction Dynamics
Reaction Pathway Analysis
Reaction Pathways
Reactive Molecular Dynamics
Recombination of Loose Ion Pairs
Replica Exchange Molecular Dynamics
Replica Exchange Molecular Dynamics (REMD)
Resonance and Molecular Dynamics
Restraint-based Molecular Dynamics
Role in Molecular Dynamics
Rossiiskii fiziologicheskii zhurnal imeni I.M. Sechenova (2005), 91(12), 1377-97, 146 Molecular dynamics simulation of dark-adapted rhodopsin and free opsin
Rotational Diffusion
Sampling limitations in molecular dynamics simulations
Significance of intramolecular isotope effect in understanding molecular dynamics
Simulated Annealing
Simulating Coordination Complexes
Simulating Molecular Collisions
Simulating reaction mechanisms
Simulating Reaction Pathways
Simulating Solvent Effects
Simulation Algorithms
Simulation Algorithms in Classical Molecular Dynamics
Simulation of Rearrangement
Simulation of Tautomerization
Simulation Protocols
Simulation Studies
Simulations
Simulations of Aromatic Systems
Software
Software Algorithms
Software Tools
Steered Molecular Dynamics (SMD)
Structure and Dynamics of Non-Rigid Molecular Systems
Temperature Control in Classical Molecular Dynamics
Temperature Effects
The Amber Molecular Dynamics Package
The journal of physical chemistry. B (2007), 111(14), 3782-8, 1437. Photochemistry of visual pigment chromophore models by ab initio molecular dynamics
The journal of physical chemistry. B (2008), 112(4), 1267-74, 1418. NMR chemical shifts of the rhodopsin chromophore in the dark state and in bathorhodopsin: a hybrid QM/MM molecular dynamics study
The journal of physical chemistry. B (2009), 113(11), 3280-91, 1398. Photodynamics in complex environments: ab initio multiple spawning quantum mechanical/molecular mechanical dynamics
Thermodynamic Integration
Thermodynamics
Time Evolution
Time Scale
Time Step
Time-resolved studies of molecular dynamics
Trajectory Analysis
Trajectory Calculations
Trajectory Simulations
Transition State Theory
Translational Diffusion
Visualization
Visualization Tools
VMD (Visual Molecular Dynamics)