Multioverlap simulations for transitions between reference configurations.

Department of Physics, Florida State University, Tallahassee, Florida 32306, USA.
Physical Review E (Impact Factor: 2.33). 10/2003; 68(3 Pt 2):036126. DOI: 10.1103/PhysRevE.68.036126
Source: PubMed

ABSTRACT We introduce a procedure to construct weight factors, which flatten the probability density of the overlap with respect to some predefined reference configuration. This allows one to overcome free-energy barriers in the overlap variable. Subsequently, we generalize the approach to deal with the overlaps with respect to two reference configurations so that transitions between them are induced. We illustrate our approach by simulations of the brain peptide Met-enkephalin with the ECEPP/2 (Empirical Conformational Energy Program for Peptides) energy function using the global-energy-minimum and the second lowest-energy states as reference configurations. The free energy is obtained as functions of the dihedral and the root-mean-square distances from these two configurations. The latter allows one to identify the transition state and to estimate its associated free-energy barrier.

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