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Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
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10.1063/1.4725183
/content/aip/journal/jcp/136/21/10.1063/1.4725183
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/21/10.1063/1.4725183
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

Representative ribbon and atomically detailed snapshots of decaalanine in vacuum are displayed along the steered path. From top to bottom, the structures correspond to: (a) a compact structure at the NN–NC distance of 13 Å, (b) the minimum energy conformation—an α-helix with an end-to-end distance of 15.2 Å, (c) a structure at the kind of the PMF shown in Fig. 2—at circa 26 Å, and (d) a coil structure at the end of one of the pulled trajectories at the end-to-end distance of 33 Å.

Image of FIG. 2.
FIG. 2.

The comparison of the PMFs obtained from the adaptive SMD method pulling at 100 Å/ns (left column of panels) and 10 Å/ns (right column of panels) when a different selection criterion is used to choose the configuration from the structures at the end of each segment. The configuration is chosen according to the JA, MW, and RC criterion and displayed in the bottom, middle and top panels, respectively. Dashed curves in red, yellow, green, brown and blue represents 50, 100, 200, 400 and 800 trajectories per segment, respectively. The solid black curve is the PMF obtained from averaging 10,000 standard SMD simulations. Note that the standard PMF for the 10 Å/ns pulling simulations (solid black curves in the right column) largely overlaps onto the reversible PMF (although not shown).

Image of FIG. 3.
FIG. 3.

The convergence of the PMF as a function of the number of sampled trajectories in ASMD (JA, MW, and RC simulations) is shown through the relative root-mean-square (RMS) error in the total free energy difference between the initial and final points. In the top panel, the reference is the reversible PMF for which the total energy difference between the end points is 21.271 kcal/mol. In the bottom panel, the reference is the SMD for which the total energy difference between the end points is 30.134 kcal/mol at 100 Å/ns pulling speed, and 21.516 kcal/mol at Å/ns pulling speed. The abscissa displays the number of trajectories along a range from 50 (=50 × 20) to 3 200 (=50 × 26). Circle data points connected by the same colored solid lines were obtained from simulation with 100 Å/ns pulling rate; whereas, square data points connected by the same colored dashed lines were obtained from simulation with 10 Å/ns pulling rate. Black, red, green represent JA, MW, RC selection criteria, respectively.

Image of FIG. 4.
FIG. 4.

The convergence of the PMF as a function of the number of sampled trajectories in ASMD (JA selection criterion) and SMD is shown through the relative root-mean-square (RMS) error in the total free energy difference between the initial and final points. As in the top panel of Fig. 3, the reference is the reversible PMF and the number of trajectories are displayed with the same scales in the abscissa. Circle data points connected by the same colored solid lines were obtained from simulation with 100 Å/ns pulling rate; whereas, square data points connected by the same colored dashed lines were obtained from simulation with 10 Å/ns pulling rate. Black and red represent ASMD (JA) and SMD, respectively.

Image of FIG. 5.
FIG. 5.

The comparison of the PMFs obtained from the adaptive SMD method pulling at 100 Å/ns (top) and 10 Å/ns (bottom) when the overall simulation window is divided into 10, 20, 40, and 80 segments.

Image of FIG. 6.
FIG. 6.

The PMFs obtained from the adaptive SMD method pulling at 100 Å/ns (top) and 10 Å/ns (bottom) are shown as a function of decaalanine end-to-end distance. The ensemble of trajectories is relaxed at constant temperature and end-to-end distance for 2 ps (red), 100 ps (green), and 200 ps (blue) between pulling segments. The solid black curve is the PMF obtained using ASMD with the JA selection criterion (and no relaxation between segments). The solid grey curve is the reversible PMF.

Image of FIG. 7.
FIG. 7.

The average number of internal hydrogen bonds in decaalanine in vacuum is shown as a function of decaalanine end-to-end distance from 100 Å/ns (top) and 10 Å/ns (bottom) pulling simulations. All curves are labeled as in Fig. 6.

Image of FIG. 8.
FIG. 8.

The average number of internal hydrogen bonds in decaalanine as a function of decaalanine end-to-end distance is shown for fast pulling (top panel) and slow pulling (bottom panel) simulations. Black represents ii + 4 (α-helix), red represents ii + 3 (310-helix), and green represents ii + 5 (π-helix). The semi-transparent curves in the top panel correspond to five additional independent simulations and indicate the spread in the error. Each of these gave rise to a PMF which is the same as that shown earlier within the resolution of the plots.

Image of FIG. 9.
FIG. 9.

Ramachandran plots of the middle eight residues (excluding the termini residues because they do not have a pair of ϕ and ψ angles) is displayed for the 100 Å/ns stretching simulations (top) for the 10 Å/ns stretching simulations (bottom) (the selection criterion is JA, the number of trajectories sampled per step is 400 for each of them). Each diagram has a total of 3200 data points: 8 ϕ-ψ angle pairs for each of the 400 trajectories. The reaction coordinate begins from top left and goes towards bottom right by walking along each row. Coloring is as follows: ALA2, black; ALA3, red; ALA4, green; ALA5, blue; ALA6, yellow; ALA7, brown; ALA8, gray; ALA9, purple.

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/content/aip/journal/jcp/136/21/10.1063/1.4725183
2012-06-07
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Adaptive steered molecular dynamics: Validation of the selection criterion and benchmarking energetics in vacuum
http://aip.metastore.ingenta.com/content/aip/journal/jcp/136/21/10.1063/1.4725183
10.1063/1.4725183
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