Spatially constrained minimization of macromolecules
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Updated: Feb 18, 2026

Spatial Separation of Molecular Conformers and Clusters
Published on: January 9, 2014
Robert E Bruccoleri1, Martin Karplus2
1Department of Biochemistry and Molecular Biology, Department of Chemistry, Harvard University, Cambridge, Massachusetts 02138.
Abstract:
A structural minimization procedure which converges rapidly and restricts the atomic shifts is outlined. It is implemented by adding a harmonic penalty term for the displacements of atomic positions and resetting the reference coordinates with respect to which the constraints are computed during the minimization. The resetting serves to reduce the constraint energy of the minimized structure to negligible levels.
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