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An improved replica-exchange sampling method: Temperature intervals with global energy reassignment
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10.1063/1.2780152
/content/aip/journal/jcp/127/16/10.1063/1.2780152
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/16/10.1063/1.2780152

Figures

Image of FIG. 1.
FIG. 1.

Mean potential energy difference between the elevated-temperature replicas and the replica as a function of quenching time. (Inset) Three representative heating-sampling-quenching cycles generated by replicas R1, R2, and R3.

Image of FIG. 2.
FIG. 2.

Radial distribution functions (RDFs) of oxygen-oxygen (O–O), oxygen-hydrogen (O–H), and hydrogen-hydrogen (H–H) atom pairs. The results of R1, R2, and R3 are shown with solid, dashed, and dotted lines, respectively. (A) RDFs for R1, R2, and R3 at respective temperature of 300, 424, and and (B) RDFs for R1, R2, and R3 after quenching for to baseline temperature of . (Inset) The magnified plot of O–O peak around .

Image of FIG. 3.
FIG. 3.

Distributions of potential energy for (A) three quenched replicas of R1, R2, and R3 at the baseline temperature (the results of R1, R2, and R3 are shown with solid, dashed, and dotted lines, respectively) and (B) 24 replicas sampled at different temperatures in REMD simulation. The bold lines in (B), which designate the REMD distributions at about 300, 430, and , show that the potential energy distributions at these temperatures exhibit a negligible degree of overlap.

Image of FIG. 4.
FIG. 4.

Conformation distributions of the alanine dipeptide in TIP3P water at sampling times of , 0.62, 4.4, and for (A) MD, (B) REMD, and (C) TIGER simulations.

Image of FIG. 5.
FIG. 5.

The conformation distribution of the alanine dipeptide in water solution generated by a TIGER simulation and the designated regions for macrostates (A) , (B) , (C) , and (D) .

Image of FIG. 6.
FIG. 6.

Evolution of the population ratios of the (solid), (dashed), (dashed-dotted), and (dotted) regions calculated from (A) MD, (B) REMD, and (C) TIGER simulations.

Image of FIG. 7.
FIG. 7.

The trajectories of , dihedral angles for (A) MD, (B) REMD, and (C) TIGER simulations for the alanine dipeptide in TIP3P water. ( plots on left, plots on right.)

Image of FIG. 8.
FIG. 8.

Convergence of the configurational-space entropy as a function of sampling time for MD (dotted line), REMD (circle), and TIGER (square) simulations. The solid lines represent the best fit of Eq. (12) to each data plot.

Tables

Generic image for table
Table I.

Population ratios (and statistical errors) averaged over the last trajectories and their associated statistical errors for the , , , and regions from the MD, REMD, and TIGER simulations.

Generic image for table
Table II.

Total number of transition of the , dihedral angles of the alanine dipeptide for REMD and TIGER simulations.

Generic image for table
Table III.

Time constants, and (in units of ns), and their standard deviations (SD) obtained from the fitting of Eq. (12) to the conformational-space entropy vs sampling time plots for the REMD and TIGER simulations.

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/content/aip/journal/jcp/127/16/10.1063/1.2780152
2007-10-31
2014-04-17
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: An improved replica-exchange sampling method: Temperature intervals with global energy reassignment
http://aip.metastore.ingenta.com/content/aip/journal/jcp/127/16/10.1063/1.2780152
10.1063/1.2780152
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