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ChemPhysChem
Article . 2022 . Peer-reviewed
License: CC BY NC ND
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ChemPhysChem
Article . 2022
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Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields

Authors: Caley Allen; Hailey R. Bureau; T. Dwight McGee; Stephen Quirk; Rigoberto Hernandez;

Benchmarking Adaptive Steered Molecular Dynamics (ASMD) on CHARMM Force Fields

Abstract

AbstractThe potentials of mean force (PMFs) along the end‐to‐end distance of two different helical peptides have been obtained and benchmarked using the adaptive steered molecular dynamics (ASMD) method. The results depend strongly on the choice of force field driving the underlying all‐atom molecular dynamics, and are reported with respect to the three most popular CHARMM force field versions: c22, c27 and c36. Two small peptides, and 1PEF, serve as the particular case studies. The comparisons between the versions of the CHARMM force fields provides both a qualitative and quantitative look at their performance in forced unfolding simulations in which peptides undergo large changes in structural conformations. We find that ASMD with the underlying c36 force field provides the most robust results for the selected benchmark peptides.

Keywords

Molecular Conformation, Molecular Dynamics Simulation, Peptides, Research Articles

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selected citations
These citations are derived from selected sources.
This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Citations provided by BIP!
popularity
This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.
BIP!Popularity provided by BIP!
influence
This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).
BIP!Influence provided by BIP!
impulse
This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.
BIP!Impulse provided by BIP!
7
Top 10%
Average
Top 10%
Green
hybrid