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Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol
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10.1063/1.3147465
/content/aip/journal/jcp/130/22/10.1063/1.3147465
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/22/10.1063/1.3147465

Figures

Image of FIG. 1.
FIG. 1.

A model for alanine dipeptide. Also shown are the main dihedral angles: , , , and . Carbon, oxygen, nitrogen, and hydrogen atoms are depicted in light green, red, blue, and gray, respectively.

Image of FIG. 2.
FIG. 2.

A schematic view of the generation of branched paths (thick lines) using the BG sampling method. The first stage involves the simulation run in the basin shown by a dotted line. Starting points for the subsequent generation of branched paths are marked with a black circle at . The second stage corresponds to the trial runs fired from ; those that reached the next interface are shown by a thick line and those which failed to reach are shown by a dotted line. For this example, having , , and , the value for point 1 at is then obtained recursively from Eq. (3): .

Image of FIG. 3.
FIG. 3.

(a) Distribution for the center of mass velocity of water molecules for MD simulations using (−) thermostat A and (●) Nosé–Hoover thermostat. (b) Time progression of the VACFs for thermostat A (−) and (●) Nosé–Hoover thermostat.

Image of FIG. 4.
FIG. 4.

Free energy landscape for blocked alanine dipeptide in vacuum at 300 K. The color scheme for the visited states changes from highest (green) to lowest (gray/blue) elevations.

Image of FIG. 5.
FIG. 5.

Free energy landscape for alanine dipeptide in explicit solvent at 300 K. The color scheme for the visited states changes from highest (gray/light blue) to lowest (black/red) elevations.

Image of FIG. 6.
FIG. 6.

Results for the FFS-MC simulations in vacuum at 300 K. (a) Free energy profile along the dihedral angle as order parameter. The dotted line corresponds to the value of at the TS. (b) Free energy landscape ( plane) where the color scheme for the visited states changes from highest (gray/light blue) to lowest (black/dark blue) elevations. The solid (black) lines correspond to the initial order parameter (state upper limit), 125 (TS), and 150 (state lower limit). The dotted (red) lines correspond to the isocommittor surface.

Image of FIG. 7.
FIG. 7.

Results for the FFS-MD simulations in vacuum at 300 K. (a) Free energy profile along the dihedral angle as order parameter. (b) Free energy landscape over the plane. Color and line schemes are the same as those indicated in the caption of Fig. 6.

Image of FIG. 8.
FIG. 8.

Density map obtained from the TPE for several FFS-MD runs for the reaction at 300 K in explicit solvent. The color scheme for the visited states changes from most (red) to least (light blue) visited region. The solid (black) lines correspond to and . Three representative trajectories are also shown.

Image of FIG. 9.
FIG. 9.

Results for the optimization process of the positioning in the FFS-MD simulation for the reaction at 300 K in explicit solvent: (a) ACFs for the angle for states collected at , 125, 120, 115, and 110 and (b) (◆) , (●) (picoseconds), and (▲) (picoseconds) curves as a function of the location of .

Image of FIG. 10.
FIG. 10.

Isocommittor surfaces obtained during the FFS-MD simulations for the reaction at 300 K in explicit solvent. The solid (black) lines correspond to and . The color scheme changes from highest (light blue) to lowest (red) elevations. The isocommittor surfaces (see Table VI) are shown for fixed values of and (solid red lines) and for fixed values of and (dotted black lines). For the data considered, is the average value observed, and are the [lower, upper] limits of the range of values observed.

Tables

Generic image for table
Table II.

Optimized sets for vacuum and explicit solvent FFS-MC and FFS-MD simulations.

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Table I.

Optimized move set for MC simulation in vacuum (Ref. 25). Parameters for the automatic optimization of move sizes (ARM and DOMC) are also given.

Generic image for table
Table III.

LSE parameters and ANOVA for the reaction coordinate model of the FFS-MC simulation in vacuum. The and angles are given in radians.

Generic image for table
Table IV.

LSE parameters and ANOVA for the reaction coordinate model of the FFS-MD simulation in vacuum. The and angles are given in radians.

Generic image for table
Table V.

LSE parameters and ANOVA for the reaction coordinate model of the slower reaction of a FFS-MD simulation in explicit solvent. The and angles are given in radians. and are given in Å and kcal/mol, respectively.

Generic image for table
Table VI.

LSE parameters and ANOVA for the reaction coordinate model of the faster reaction from a FFS-MD simulation in explicit solvent. The and angles are given in radians. and are given in Å and kcal/mol, respectively.

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/content/aip/journal/jcp/130/22/10.1063/1.3147465
2009-06-08
2014-04-21
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Kinetics and reaction coordinate for the isomerization of alanine dipeptide by a forward flux sampling protocol
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/22/10.1063/1.3147465
10.1063/1.3147465
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