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Communication: Simulated tempering with fast on-the-fly weight determination
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Figures

Image of FIG. 1.

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FIG. 1.

ST simulation of the 1D system with on-the-fly weights determination. (a) Time evolution of the weights during ST. (b) Exact weights. (c) Change of temperatures during ST. (d) Temperature distribution. Time evolution (e) and distribution (f) of the positions of both particles at T = 0.2. (f) Results obtained from ST (black) and analytical calculation (red).

Image of FIG. 2.

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FIG. 2.

Short time window of the ST trajectory of the 1D system. (a) Time evolution of the coordinates of two particles, and (b) fluctuation of the instantaneous energy around the average energy at T 1 = 0.2. (c) Change of temperatures during ST. (d) Time evolution of two selected weights corresponding to T 2 = 0.3 (black) and T 3 = 0.4 (red).

Image of FIG. 3.

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FIG. 3.

ST simulation of Ala20 with on-the-fly weights determination. (a) Time evolution of the weights during ST. (b) Weights obtained from 100 ns REMD. (c) Change of temperatures during ST. (d) Temperature distribution. Time evolution (e) and distribution (f) of the RMSD at T = 300 K. (f) Results obtained from ST (black) and REMD (red) simulations. The structures corresponding to the two dominant peaks are shown.

Image of FIG. 4.

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FIG. 4.

ST simulation of the (Aβ16−22)3 system with on-the-fly weights determination. (a) Time evolution of the weights during ST. (b) Weights obtained from 100 ns REMD. (c) Change of temperatures during ST. (d) Distribution of the order parameter P2 at T = 300 K. (d) Results obtained from ST (black) and REMD (red). The structures corresponding to the two dominant peaks are shown.

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/content/aip/journal/jcp/138/6/10.1063/1.4792046
2013-02-12
2014-04-21

Abstract

We propose an efficient method to enhance sampling in computer simulations by combining the simulated tempering algorithm with a fast on-the-fly weight determination scheme. The weights are self-updated via a trapezoid rule during the simulated tempering simulation. With our proposed scheme, simulated tempering requires neither prior trial simulations nor complicated update schemes. The advantage of our method over replica exchange molecular dynamics has been demonstrated with the study of the folding of the 20-residue alanine peptide and the aggregation of a trimer formed by the Alzheimer's peptide fragment Aβ16−22.

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Scitation: Communication: Simulated tempering with fast on-the-fly weight determination
http://aip.metastore.ingenta.com/content/aip/journal/jcp/138/6/10.1063/1.4792046
10.1063/1.4792046
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