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Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations
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10.1063/1.2901037
/content/aip/journal/jcp/128/13/10.1063/1.2901037
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/13/10.1063/1.2901037
View: Figures

Figures

Image of FIG. 1.
FIG. 1.

The potential energy surface for the model system. The potential energy function is given in units of and takes a functionThe separation of contour lines (different colors) is . The grids are given for illustration. In the calculations the size of the small areas is .

Image of FIG. 2.
FIG. 2.

The convergence of with different initial guesses.

Image of FIG. 3.
FIG. 3.

The calculated free energy surface for the model system. The free energy (in units of and the separation between contour lines is ) was calculated using the non-Boltzmann distribution approach using 40 different temperatures ranging between and .

Image of FIG. 4.
FIG. 4.

The ratio of the successful over total trajectories increases with the adaptive kinetic sampling steps. The trajectory length is .

Image of FIG. 5.
FIG. 5.

The natural logarithm of visiting probability by the successful trajectories (calculated after reweighting of their initial configurations according to a Boltzmann distribution at the temperature ). The separation between contour lines is .

Image of FIG. 6.
FIG. 6.

An example of the sampled spatial points (black) and those that lead to successful trajectories (red). The sampling thus not allows calculation of thermodynamic properties at the desired temperature (the points at the center) but also covers with a high probability that reaction portion of the configuration space.

Image of FIG. 7.
FIG. 7.

The calculated rate as a function of the length of trajectories (the trajectories are obtained with a constant energy using Newtonian equations).

Image of FIG. 8.
FIG. 8.

The convergence of for a simulation for maltose. It can be seen that they converge in a short simulation of a few picoseconds. In comparison, their convergence took about when the previous updating method was used (Ref. 26).

Image of FIG. 9.
FIG. 9.

(a) The sampled energy for a large system (kinase in explicit solvent with 19 179 atoms) using the enhanced sampling method (dashed line) and normal MD simulations (solid line). (b) The energy distribution is significantly broadened in the enhanced sampling simulations (dashed line) compared to the normal MD (solid line).

Image of FIG. 10.
FIG. 10.

The potential of mean force (dashed line) as a function of the coordinate, which shows a lower barrier compared to that obtained along the pathway with the lower barrier (calculated using configurations with ).

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/content/aip/journal/jcp/128/13/10.1063/1.2901037
2008-04-07
2014-04-25
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Self-adaptive enhanced sampling in the energy and trajectory spaces: Accelerated thermodynamics and kinetic calculations
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/13/10.1063/1.2901037
10.1063/1.2901037
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