Variational approach for minimizing LennardJones energies
(1996) In Physical Review E  Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 53(2). p.17251731 Abstract
A variational method for computing conformational properties of molecules with LennardJones potentials for the monomermonomer 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 shortdistance behavior of the LennardJones 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 densepacked 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 LennardJones potentials for the monomermonomer 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 shortdistance behavior of the LennardJones 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 densepacked 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 densepacked 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
 1063651X
 language
 English
 LU publication?
 yes
 id
 a31f228763a34c32b5f6b1dcda9e9046
 date added to LUP
 20161003 19:17:06
 date last changed
 20170110 14:58:57
@article{a31f228763a34c32b5f6b1dcda9e9046, abstract = {<p>A variational method for computing conformational properties of molecules with LennardJones potentials for the monomermonomer 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 shortdistance behavior of the LennardJones 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 densepacked 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 densepacked 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 = {1063651X}, language = {eng}, number = {2}, pages = {17251731}, publisher = {American Physical Society}, series = {Physical Review E  Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics}, title = {Variational approach for minimizing LennardJones energies}, volume = {53}, year = {1996}, }