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Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study
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10.1063/1.2794763
/content/aip/journal/jcp/127/17/10.1063/1.2794763
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/17/10.1063/1.2794763

Figures

Image of FIG. 1.
FIG. 1.

Alanine dipeptide molecule.

Image of FIG. 2.
FIG. 2.

Plot of psi (left) and phi (right) angles of the alanine dipeptide during the normal MD simulations at (a) and (b) .

Image of FIG. 3.
FIG. 3.

Plot of psi (left) and phi (right) angles of the alanine dipeptide during the accelerated MD simulations: (a) , ; (b) , ; and (c) , .

Image of FIG. 4.
FIG. 4.

Plot of psi (left) and phi (right) angles of the alanine dipeptide during the accelerated MD simulations: (a) , ; (b) , ; and (c) , .

Image of FIG. 5.
FIG. 5.

(Color) Free energy plots for the transitions along the phi and psi angles of the alanine dipeptide: (left) contour density plot and (right) surface plot in units of .

Image of FIG. 6.
FIG. 6.

(Color) Free energy plots for the transitions along the phi and psi angles of the alanine dipeptide: (left) contour density plot and (right) surface plot in units of .

Image of FIG. 7.
FIG. 7.

(Color) Free energy plots for the transitions along the phi and psi angles of the alanine dipeptide: (left) contour density plot and (right) surface plot in units of .

Image of FIG. 8.
FIG. 8.

Unweighted free energy profile of psi torsional angle obtained from accelerated MD at eight different values of . The lower the barrier, the smaller the .

Image of FIG. 9.
FIG. 9.

(Color) Exponential decay of the probability distribution of the survival time in the free energy well defined by calculated from normal MD at and accelerated MD with eight different values of .

Image of FIG. 10.
FIG. 10.

Plot calculated from eight accelerated MD simulations relating the escaping rate , barrier height , and angular frequencies and with the boost potential .

Tables

Generic image for table
Table I.

Summary of the data collected from the normal MD simulations (at 300 and ) and accelerated MD simulations at different values of ..

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/content/aip/journal/jcp/127/17/10.1063/1.2794763
2007-11-07
2014-04-16
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Estimating kinetic rates from accelerated molecular dynamics simulations: Alanine dipeptide in explicit solvent as a case study
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/17/10.1063/1.2794763
10.1063/1.2794763
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