Variational approach for minimizing Lennard-Jones energies

Summary, in English

A variational method for computing conformational properties of molecules with Lennard-Jones potentials for the monomer-monomer interactions is presented. The approach is tailored to deal with angular degrees of freedom, rotors, and consists of the iterative solution of a set of deterministic equations with an annealing in temperature. The singular short-distance behavior of the Lennard-Jones potential is adiabatically switched on in order to obtain stable convergence. As testbeds for the approach two distinct ensembles of molecules are used, characterized by a roughly dense-packed or a more elongated ground state. For the latter, problems are generated from natural frequencies of occurrence of amino acids and phenomenologically determined potential parameters; they seem to represent less disorder than was previously assumed in synthetic protein studies. For the dense-packed problems in particular, the variational algorithm clearly outperforms a gradient descent method in terms of minimal energies. Although it cannot compete with a careful simulating annealing algorithm, the variational approach requires only a tiny fraction of the computer time. Issues and results when applying the method to polyelectrolytes at a finite temperature are also briefly discussed.

• Författare: Carsten Peterson; Ola Sommelius; Bo Söderberg
• Avdelning/ar: Computational Biology and Biological Physics
• Publiceringsår: 1996
• Språk: Engelska
• Sidor: 1725-1731
• Publikation/Tidskrift/Serie: Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
• Volym: 53
• Issue: 2
• Dokumenttyp: Artikel i tidskrift
• Förlag: American Physical Society
• Aktiv: Published
• ISBN/ISSN/Övrigt: ISSN: 1063-651X