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Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces
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10.1063/1.2354157
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    Affiliations:
    1 School of Computational Science, Florida State University, Tallahassee, Florida 32306
    2 Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306
    3 School of Computational Science, Florida State University, Tallahassee, Florida 32306; Department of Physics, Florida State University, Tallahassee, Florida 32306; and Theoretical Biophysics Laboratory, Department of Physics, Nagoya University, 464-8602 Japan
    4 Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306; Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306; and School of Computational Science, Florida State University, Tallahassee, Florida 32306
    a) Electronic mail: berg@scs.fsu.edu
    b) Electronic mail: yang@sb.fsu.edu
    J. Chem. Phys. 125, 144902 (2006); http://dx.doi.org/10.1063/1.2354157
/content/aip/journal/jcp/125/14/10.1063/1.2354157
http://aip.metastore.ingenta.com/content/aip/journal/jcp/125/14/10.1063/1.2354157
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Torsional potential for “butanelike” molecule used as model system. Solid line represents unscaled potential for this butanelike molecule; dash line represents scaled potential potential . Exchange occurring when replicas are in the same conformational region as unproductive one for canonical sampling, while one occurring when replicas are in the different conformational region is productive exchange.

Image of FIG. 2.
FIG. 2.

Efficiency comparison between FRREM and REM in “butanelike” model system. (a) Dihedral angle changes as function of simulation time. (b) Time evolution of ratio of cumulative distribution of dihedral angle in the range (0, 180). (c) Time evolution of standard deviation for ratio of cumulative distribution of dihedral angle in the range (0,180). The results from FRREM are labeled by open circle and dotted line and those from REM are labeled by solid circle and solid line.

Image of Scheme 1.
Scheme 1.

Suggested designs for FRREM simulation. (a) Finite reservoir is set in the middle of two “temperature” runs. (b) Flexible combination of finite reservoirs with real time simulations.

Image of FIG. 3.
FIG. 3.

Time evolution of computed potential of mean forces around leucine angle using three different sampling methods. (a) Using regular REM. (b) Using one CPU FRREM. (c) Using two-CPU FRREM. Potential of mean forces were computed based on occurrence probability in the simulations on unscaled potential.

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/content/aip/journal/jcp/125/14/10.1063/1.2354157
2006-10-10
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Finite reservoir replica exchange to enhance canonical sampling in rugged energy surfaces
http://aip.metastore.ingenta.com/content/aip/journal/jcp/125/14/10.1063/1.2354157
10.1063/1.2354157
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