The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.
Description
Local elevation: A method for improving the searching properties of molecular dynamics simulation | SpringerLink
%0 Journal Article
%1 Huber1994LocalElevation
%A Huber, Thomas
%A Torda, Andrew E.
%A van Gunsteren, Wilfred F.
%D 1994
%J Journal of Computer-Aided Molecular Design
%K enhanced-sampling local-elevation path-sampling
%N 6
%P 695--708
%R 10.1007/BF00124016
%T Local elevation: A method for improving the searching properties of molecular dynamics simulation
%U http://dx.doi.org/10.1007/BF00124016
%V 8
%X The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.
@article{Huber1994LocalElevation,
abstract = {The concept of memory has been introduced into a molecular dynamics algorithm. This was done so as to persuade a molecular system to visit new areas of conformational space rather than be confined to a small number of low-energy regions. The method is demonstrated on a simple model system and the 11-residue cyclic peptide cyclosporin A. For comparison, calculations were also performed using simulated temperature annealing and a potential energy annealing scheme. Although the method can only be applied to systems with a small number of degrees of freedom, it offers the chance to generate a multitude of different low-energy structures, where other methods only give a single one or few. This is clearly important in problems such as drug design, where one is interested in the conformational spread of a system.},
added-at = {2017-05-03T04:36:10.000+0200},
author = {Huber, Thomas and Torda, Andrew E. and van Gunsteren, Wilfred F.},
biburl = {https://www.bibsonomy.org/bibtex/2552438188b82f36338237bbad6a533d0/salotz},
description = {Local elevation: A method for improving the searching properties of molecular dynamics simulation | SpringerLink},
doi = {10.1007/BF00124016},
interhash = {50ac37a90a95f522cd9b50601ca31749},
intrahash = {552438188b82f36338237bbad6a533d0},
issn = {1573-4951},
journal = {Journal of Computer-Aided Molecular Design},
keywords = {enhanced-sampling local-elevation path-sampling},
number = 6,
pages = {695--708},
timestamp = {2017-05-03T04:36:10.000+0200},
title = {Local elevation: A method for improving the searching properties of molecular dynamics simulation},
url = {http://dx.doi.org/10.1007/BF00124016},
volume = 8,
year = 1994
}