Improved interaction potentials for charged residuals in proteins

Article Abstract:

Accurate free energies involving charged groups from molecular simulations are obtained from reoptimizing OPLS-AA parameters by using Monte Carlo free energy perturbation. The new parameters are used directly in molecular simulations without any modification of neutral residues and are important in simulations where charged residues have changed the environment.

Thermal properties, Gibbs' free energy, Monte Carlo method, Monte Carlo methods, Mechanical properties

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Simulation of an ensemble of conformational transitions in a united-residue model of calmodulin

Article Abstract:

The complete dynamical simulation of the structural transition of calmoulin is examined. A simple residue-level computer model of calmoudulin's N-terminal lobe results in a statistically converged ensemble of dynamic conformational transitions.

Transition metals, Simulation methods, Simulation, Calmodulin

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On the structural convergence of biomolecular simulations by determination of the effective sample size

Article Abstract:

The use of the assessment of the effective sample size of proteins and other biological systems in studying their structural convergence is analyzed.

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