Abstract
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.
Acknowledgements
The authors thank P. Hünenberger and H. Hansen for fruitful discussions. Use of the HPC cluster Wiglaf at the Department of Physics of the University of Trento is acknowledged. The authors are member of the Interdisciplinary Laboratory of Computational Science (LISC).