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Accelerated entropy estimates with accelerated dynamics
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10.1063/1.2794754
/content/aip/journal/jcp/127/15/10.1063/1.2794754
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2794754
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

(Color) Quartic double-well potential with a barrier of (thick black line) and several biased potentials. The threshold boost energy is fixed at and is 5, 10, 15, 25, 50, or , in decreasing magnitude of boost.

Image of FIG. 2.
FIG. 2.

(Color) Quartic double-well potential with a barrier of (thick black line) and several biased potentials. The threshold boost energy is fixed at and is 5, 10, 15, 25, 50, or , in decreasing magnitude of boost.

Image of FIG. 3.
FIG. 3.

(Color) Mean entropy as a function of elapsed time using normal and accelerated molecular dynamics on a quartic double-well potential with a barrier of . The numerical entropy of 4.05 is shown as a thick black line. Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 1.

Image of FIG. 4.
FIG. 4.

(Color) Standard deviation of entropy estimates as a function of elapsed time using normal and accelerated molecular dynamics on a quartic double-well potential with a barrier of . Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 1.

Image of FIG. 5.
FIG. 5.

(Color) Mean entropy as a function of elapsed time using normal and accelerated molecular dynamics on a quartic double-well potential with a barrier of . The numerical entropy of 3.26 is shown as a thick black line. Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 2.

Image of FIG. 6.
FIG. 6.

(Color) Standard deviation of entropy estimates as a function of time using normal and accelerated molecular dynamics on a quartic double-well potential with a barrier of . Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 2.

Image of FIG. 7.
FIG. 7.

(Color) Two-dimensional double-well potential with a barrier of . The principal components analysis eigenvectors from a normal molecular dynamics simulation are indicated by dashed white lines.

Image of FIG. 8.
FIG. 8.

(Color) Mean entropy as a function of elapsed time using normal and accelerated molecular dynamics on a two-dimensional double-well potential with a barrier of . The entropy is calculated using a two-dimensional probability density estimate from a histogram. The numerical entropy of 5.59 is shown as a thick black line. Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 2.

Image of FIG. 9.
FIG. 9.

(Color) Standard deviation of entropy estimates as a function of time using normal and accelerated molecular dynamics on a two-dimensional double-well potential with a barrier of . The entropy is calculated using a two-dimensional probability density estimate from a histogram. Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 2.

Image of FIG. 10.
FIG. 10.

(Color) Mean entropy as a function of elapsed time using normal and accelerated molecular dynamics on a two-dimensional double-well potential with a barrier of . The entropy is calculated using two one-dimensional probability density estimates from histograms of projections into principal components analysis space. The numerical entropy of 5.59 is shown as a thick black line. Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 2.

Image of FIG. 11.
FIG. 11.

(Color) Standard deviation of entropy estimates as a function of time using normal and accelerated molecular dynamics on a two-dimensional double-well potential with a barrier of . The entropy is calculated using two one-dimensional probability density estimates from histograms of projections into principal components analysis space. Results from normal MD are shown by a dashed blue line and accelerated MD results are solid lines colored as in Fig. 2.

Image of FIG. 12.
FIG. 12.

(Color online) Entropy estimates using normal and accelerated molecular dynamics on an eight-residue peptide. The entropy is calculated using one-dimensional probability density estimates from histograms of projections into principal components analysis space. From bottom to top, the entropy estimates are for normal MD, AMD applied to the peptide torsion angles, AMD applied to both the torsional angles and the total potential, and AMD for a larger boost on both.

Image of FIG. 13.
FIG. 13.

(Color online) Entropy estimates using normal and accelerated molecular dynamics on an eight-residue peptide. The entropy is calculated using quasiharmonic analysis. The key is as in Fig. 12.

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/content/aip/journal/jcp/127/15/10.1063/1.2794754
2007-10-16
2014-04-19
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Accelerated entropy estimates with accelerated dynamics
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/15/10.1063/1.2794754
10.1063/1.2794754
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