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Diffusive Langevin Dynamics
Inertial Langevin Dynamics
Thermal Motion of Proteins in Crystals and in Solution
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32 time slice a-helix alanine alanine dipeptide algorithm appear atomic fluctuations average behavior bond lengths BPTI calculated chapter Chem conformation space constrained multiple copy covalent bond crystal contacts crystal simulation crystallography decreases degrees of freedom deviations diffusive Langevin Doniach effect energy landscape ensemble equilibration equilibrium experimental explicit water molecules explore folding process folding trajectories force formation global motion hairpin helical peptide helix hydrogen bonds hydrophobic contacts initial trajectory isotropic B-factors iterations Karplus kcal/mol Langevin dynamics Langevin equation lengths and angles magnitude method Molecular Dynamics Molecular Dynamics Simulations multiple copy refinement multiple time step nanoseconds nonbonded contacts nonbonded interactions P-hairpin Pancreatic Trypsin Inhibitor path length peptide Phys potential function principle components problem protein folding range of motion Reaction Path Annealing scale secondary structure shown in Figure significantly simulated annealing slice trajectories small number solution simulations solvent temperature thermodynamic transition unit cell water molecules