Pickett angles and Cremer-Pople coordinates as collective variables for the enhanced sampling of six-membered ring conformations

Although completely equivalent for the description of puckered ring conformers, the two popular coordinates sets of Strauss-Pickett dihedral angles and Cremer-Pople spherical coordinates are shown to have contrasting features when employed as collective variables in free-energy calculations with acc...

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Bibliographic Details
Published in:Molecular physics 2011-01, Vol.109 (1), p.141-148
Main Authors: Sega, M., Autieri, E., Pederiva, F.
Format: Article
Language:English
Subjects:
Equivalence
free energy
Glucose
Mathematical analysis
Mineralogy
Minerals
Molecular dynamics
Molecular physics
puckering
ring conformers
Sampling
Sampling techniques
Simulation
Spherical coordinates
sugars
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Summary:Although completely equivalent for the description of puckered ring conformers, the two popular coordinates sets of Strauss-Pickett dihedral angles and Cremer-Pople spherical coordinates are shown to have contrasting features when employed as collective variables in free-energy calculations with accelerated sampling techniques. Results from a 100 ns molecular dynamics simulation at conformational equilibrium and from combined metadynamics/umbrella sampling calculations of glucose are exploited to elucidate these differences.
ISSN:0026-8976
1362-3028
DOI:10.1080/00268976.2010.522208