Structure conjugate gradient minimization

Stich, R. Car, M. Parrinello, and S. Baroni, Conjugate gradient minimization of the energy functional A new method for electronic structure calculation, Phys. Rev. B Condens. Matter, 39 (1989), 4997-5004. 

Figure 3. The segment consisting of residues Cys-192 and His-193 of the 2.8 A resolution structure of a single site mutant of aspartate aminotransferase [23]. Superimposed are the initial structure (dotted lines) obtained by fitting the atomic model to a multiple isomorphous replacement map, the structure obtained after several cycles of rebuilding and restrained least-squares refinement (thick lines), the structure obtained after simulated annealing refinement (thin lines), and the structure obtained after conjugate gradient minimization (dashed lines).

Energy minimization methods that exploit information about the second derivative of the potential are quite effective in the structural refinement of proteins. That is, in the process of X-ray structural determination one sometimes obtains bad steric interactions that can easily be relaxed by a small number of energy minimization cycles. The type of relaxation that can be obtained by energy minimization procedures is illustrated in Fig. 4.4. In fact, one can combine the potential U r) with the function which is usually optimized in X-ray structure determination (the R factor ) and minimize the sum of these functions (Ref. 4) by a conjugated gradient method, thus satisfying both the X-ray electron density constraints and steric constraint dictated by the molecular potential surface. 

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