“C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions.”
“The time step of the free MD simulations was 2 fs, with a cutoff of 13 Å for the nonbonded interaction, and SHAKE”
“However, it should be considered that calculation of the native nonbonded energy using the first eigenvalue and associated eigenvector is a simplified approximation of the complex and rough energy landscape of a protein.”
“At a second stage, the best solutions were submitted to a simulated annealing (SA) procedure with all nonbonded interactions on all free protein side-chains and the tethered backbone.”
“Meanwhile the oxygen atom has lone pairs of nonbonded electrons that render it weakly basic in the presence of strong acids such as sulfuric acid.”
“Colovos C, Yeates TO (1993) Verification of protein structures: patterns of nonbonded atomic interactions.”
“For the nonbonded interactions, an extended electrostatic treatment was applied with the electrostatic interactions within 12 Å described by group-based coulombic interactions.”
“ was used for multiple time-stepping: 4 fs for the long-range electrostatic forces, 2 fs for short-range nonbonded forces, and 1 fs for bonded forces.”
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