Long Time Scale Computer Simulations of ProteinsStanford University, 2000 - 220 pages |
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12 Residue 32 time slice alanine alanine dipeptide algorithm appear atomic fluctuations 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 energy landscape ensemble equilibration equilibrium experimental explicit water molecules explore folding process folding trajectories force formation global motion helical peptide helix hydrate hydrogen bonds hydrophobic contacts initial trajectory isotropic B-factors iterations 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 Pancreatic Trypsin Inhibitor path length peptide Phys potential function principle components problem protein folding radius of gyration Reaction Path Annealing scale secondary structure shown in Figure significantly simulated annealing slice trajectories small number solution simulations solvent ẞ-hairpin temperature thermodynamic transition unit cell water molecules