Variational approach for minimizing Lennard-Jones energies
(1996) In Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics 53(2). p.1725-1731- Abstract
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... (More)
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.
(Less)
- author
- Peterson, Carsten LU ; Sommelius, Ola LU and Söderberg, Bo LU
- organization
- publishing date
- 1996
- type
- Contribution to journal
- publication status
- published
- in
- Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics
- volume
- 53
- issue
- 2
- pages
- 7 pages
- publisher
- American Physical Society
- external identifiers
-
- scopus:5344252329
- ISSN
- 1063-651X
- language
- English
- LU publication?
- yes
- id
- a31f2287-63a3-4c32-b5f6-b1dcda9e9046
- date added to LUP
- 2016-10-03 19:17:06
- date last changed
- 2022-12-14 02:58:12
@article{a31f2287-63a3-4c32-b5f6-b1dcda9e9046,
abstract = {{<p>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.</p>}},
author = {{Peterson, Carsten and Sommelius, Ola and Söderberg, Bo}},
issn = {{1063-651X}},
language = {{eng}},
number = {{2}},
pages = {{1725--1731}},
publisher = {{American Physical Society}},
series = {{Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics}},
title = {{Variational approach for minimizing Lennard-Jones energies}},
volume = {{53}},
year = {{1996}},
}