Adaptive umbrella sampling of the potential energy: modified updating procedure of the umbrella potential and application to peptide folding |
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Authors: | Christian Bartels Michael Schaefer Martin Karplus |
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Institution: | (1) Laboratoire de Chimie Biophysique, Institut Le Bel, Université Louis Pasteur, 4 rue Blaise Pascal, F-67000 Strasbourg, France, FR;(2) Department of Chemistry, Harvard University, Cambridge, MA 02138, USA, US |
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Abstract: | Adaptive umbrella sampling of the potential energy is used as a search method to determine the structures and thermodynamics
of peptides in solution. It leads to uniform sampling of the potential energy, so as to combine sampling of low-energy conformations
that dominate the properties of the system at room temperature with sampling of high-energy conformations that are important
for transitions between different minima. A modification of the procedure for updating the umbrella potential is introduced
to increase the number of transitions between folded and unfolded conformations. The method does not depend on assumptions
about the geometry of the native state. Two peptides with 12 and 13 residues, respectively, are studied using the CHARMM polar-hydrogen
energy function and the analytical continuum solvent potential for treatment of solvation. In the original adaptive umbrella
sampling simulations of the two peptides, two and six transitions occur between folded and unfolded conformations, respectively,
over a simulation time of 10 ns. The modification increases the number of transitions to 6 and 12, respectively, in the same
simulation time. The precision of estimates of the average effective energy of the system as a function of temperature and
of the contributions to the average effective energy of folded conformations obtained with the adaptive methods is discussed.
Received: 11 July 1998 / Accepted: 22 September 1998 / Published online: 17 December 1998 |
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Keywords: | : Adaptive umbrella sampling Multicanonical sampling Helical peptide β -hairpin |
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