Matches in SemOpenAlex for { <https://semopenalex.org/work/W4210916755> ?p ?o ?g. }
- W4210916755 endingPage "1422" @default.
- W4210916755 startingPage "1406" @default.
- W4210916755 abstract "The string method with swarms of trajectories (SMwST) is an algorithm that identifies a physically meaningful transition pathway─a one-dimensional curve, embedded within a high-dimensional space of selected collective variables. The SMwST algorithm leans on a series of short, unbiased molecular dynamics simulations spawned at different locations of the discretized path, from whence an average dynamic drift is determined to evolve the string toward an optimal pathway. However conceptually simple in both its theoretical formulation and practical implementation, the SMwST algorithm is computationally intensive and requires a careful choice of parameters for optimal cost-effectiveness in applications to challenging problems in chemistry and biology. In this contribution, the SMwST algorithm is presented in a self-contained manner, discussing with a critical eye its theoretical underpinnings, applicability, inherent limitations, and use in the context of path-following free-energy calculations and their possible extension to kinetics modeling. Through multiple simulations of a prototypical polypeptide, combining the search of the transition pathway and the computation of the potential of mean force along it, several practical aspects of the methodology are examined with the objective of optimizing the computational effort, yet without sacrificing accuracy. In light of the results reported here, we propose some general guidelines aimed at improving the efficiency and reliability of the computed pathways and free-energy profiles underlying the conformational transitions at hand." @default.
- W4210916755 created "2022-02-09" @default.
- W4210916755 creator A5003813261 @default.
- W4210916755 creator A5006985610 @default.
- W4210916755 creator A5010656224 @default.
- W4210916755 creator A5046732533 @default.
- W4210916755 creator A5067685274 @default.
- W4210916755 creator A5071912456 @default.
- W4210916755 creator A5076283101 @default.
- W4210916755 creator A5080873196 @default.
- W4210916755 date "2022-02-09" @default.
- W4210916755 modified "2023-10-14" @default.
- W4210916755 title "A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls" @default.
- W4210916755 cites W185137928 @default.
- W4210916755 cites W1963739311 @default.
- W4210916755 cites W1969256423 @default.
- W4210916755 cites W1971008678 @default.
- W4210916755 cites W1976660933 @default.
- W4210916755 cites W1976998887 @default.
- W4210916755 cites W1978607920 @default.
- W4210916755 cites W1979348555 @default.
- W4210916755 cites W1980055293 @default.
- W4210916755 cites W1981919747 @default.
- W4210916755 cites W1984853348 @default.
- W4210916755 cites W1986614779 @default.
- W4210916755 cites W1994158181 @default.
- W4210916755 cites W1998299443 @default.
- W4210916755 cites W1998404217 @default.
- W4210916755 cites W2001087198 @default.
- W4210916755 cites W2001294077 @default.
- W4210916755 cites W2001398410 @default.
- W4210916755 cites W2003225059 @default.
- W4210916755 cites W2010347742 @default.
- W4210916755 cites W2011189520 @default.
- W4210916755 cites W2014574246 @default.
- W4210916755 cites W2018745854 @default.
- W4210916755 cites W2032373538 @default.
- W4210916755 cites W2032518047 @default.
- W4210916755 cites W2033228675 @default.
- W4210916755 cites W2034588787 @default.
- W4210916755 cites W2040249893 @default.
- W4210916755 cites W2048633418 @default.
- W4210916755 cites W2049738344 @default.
- W4210916755 cites W2053081979 @default.
- W4210916755 cites W2054498139 @default.
- W4210916755 cites W2064556178 @default.
- W4210916755 cites W2065281489 @default.
- W4210916755 cites W2071259484 @default.
- W4210916755 cites W2075154176 @default.
- W4210916755 cites W2081555206 @default.
- W4210916755 cites W2086817352 @default.
- W4210916755 cites W2093018891 @default.
- W4210916755 cites W2097951193 @default.
- W4210916755 cites W2099490136 @default.
- W4210916755 cites W2102375526 @default.
- W4210916755 cites W2103607079 @default.
- W4210916755 cites W2119546621 @default.
- W4210916755 cites W2128930058 @default.
- W4210916755 cites W2130390906 @default.
- W4210916755 cites W2132589721 @default.
- W4210916755 cites W2143171629 @default.
- W4210916755 cites W2149655632 @default.
- W4210916755 cites W2156480395 @default.
- W4210916755 cites W2158323088 @default.
- W4210916755 cites W2246932694 @default.
- W4210916755 cites W2265732782 @default.
- W4210916755 cites W2321294576 @default.
- W4210916755 cites W2323586060 @default.
- W4210916755 cites W2326817751 @default.
- W4210916755 cites W2326979787 @default.
- W4210916755 cites W2346590986 @default.
- W4210916755 cites W2404280981 @default.
- W4210916755 cites W2463208053 @default.
- W4210916755 cites W2528743173 @default.
- W4210916755 cites W2548311158 @default.
- W4210916755 cites W2559781202 @default.
- W4210916755 cites W2563321337 @default.
- W4210916755 cites W2574160838 @default.
- W4210916755 cites W2588867992 @default.
- W4210916755 cites W2592925374 @default.
- W4210916755 cites W2612790657 @default.
- W4210916755 cites W2623055862 @default.
- W4210916755 cites W2625185182 @default.
- W4210916755 cites W2747329020 @default.
- W4210916755 cites W2765861397 @default.
- W4210916755 cites W2804422193 @default.
- W4210916755 cites W2885128148 @default.
- W4210916755 cites W2890208798 @default.
- W4210916755 cites W2901832678 @default.
- W4210916755 cites W2913076418 @default.
- W4210916755 cites W2949765518 @default.
- W4210916755 cites W2953326364 @default.
- W4210916755 cites W2968909424 @default.
- W4210916755 cites W2982862739 @default.
- W4210916755 cites W3025988887 @default.
- W4210916755 cites W3046751266 @default.
- W4210916755 cites W3092637873 @default.
- W4210916755 cites W3097292324 @default.