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Multidimensional generalized-ensemble algorithms for complex systems
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10.1063/1.3127783
/content/aip/journal/jcp/130/21/10.1063/1.3127783
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/21/10.1063/1.3127783

Figures

Image of FIG. 1.
FIG. 1.

Time series of the labels of , , (a) and , , (b) as functions of MC sweeps, and that of both and for the region from 400 000 MC sweeps to 700 000 MC sweeps (c). The results were from one of the replicas (replica 1). In (a) and (b), MC sweeps start at 100 000 and end at 1 100 000 because the first 100 000 sweeps have been removed from the consideration for thermalization purpose.

Image of FIG. 2.
FIG. 2.

Time series of the temperature (a), total energy (b), conformational energy (c), solvation free energy (d), and end-to-end distance (e) for the same replica as in Fig. 1. The temperature is in K, the energy is in kcal/mol, and the end-to-end distance is in Å.

Image of FIG. 3.
FIG. 3.

Contour curves and histograms of distributions of the total energy and the solvation free energy [(a) and (b)] from the two-dimensional REM simulation.

Image of FIG. 4.
FIG. 4.

The average total energy (a), average conformational energy (b), average of (c), and average end-to-end distance (d) with all the values as functions of temperature. The lines colored in red, green, blue, and purple are for , , , and , respectively.

Image of FIG. 5.
FIG. 5.

The dimensionless free energy as a function of labels of temperature, , obtained by the two-dimensional REM simulation. The four curves correspond to , and 4 from top to bottom.

Image of FIG. 6.
FIG. 6.

Time series of the labels of , i.e., (a) and , i.e., (b) as functions of MC sweeps, and those of both and for the region from 350 000 MC sweeps to 550 000 MC sweeps (c). In (a) and (b), MC sweeps start at 100 000 and end at 1 100 000 because the first 100 000 sweeps have been removed from the consideration for thermalization.

Image of FIG. 7.
FIG. 7.

Histogram of the distribution of the labels of , , and , , obtained by the two-dimensional ST simulation.

Image of FIG. 8.
FIG. 8.

Time series of the temperature (a), total energy (b), conformational energy (c), solvation free energy (d), and end-to-end distance (e) for the two-dimensional ST simulation.

Image of FIG. 9.
FIG. 9.

The average total energy (a), average conformational energy (b), average of (c), and average end-to-end distance (d) with all the values as functions of temperature. The lines colored in red, green, blue, and purple are for , , , and , respectively.

Image of FIG. 10.
FIG. 10.

Time series of the total energy [(a) and (b)], conformational energy [(c) and (d)], and solvation free energy [(e) and (f)] with (in gas phase) and with (in aqueous solution), respectively. The red, green, and blue curves are for the fixed temperatures (300 K), (549 K), and (700 K), respectively. In gas phase, the total energy of (a) is the same as the conformational energy of (c). The scales of the ordinate in (a) and (c) are different from each other.

Image of FIG. 11.
FIG. 11.

The lowest-total-energy conformations obtained at the lowest temperature (300 K) with (in gas phase) (a) and (in aqueous solution) (b), and the two super imposed conformations (c). VMD software (Ref. 86) and RASTER 3D software (Ref. 87) were used to create the figures. The solid spheres are the oxygen atoms (in red) and the nitrogen atoms (in blue) in Table V.

Image of FIG. 12.
FIG. 12.

The atomistic solvation free energy as a function of labels of heavy atoms for the lowest-total-energy conformations obtained at the lowest temperature (300 K) with (in gas phase) and (in aqueous solution).

Image of FIG. 13.
FIG. 13.

Snapshots at 200 000 MC sweeps [(a) and (d)], at 600 000 MC sweeps [(b) and (e)], and at 1 000 000 MC sweeps [(c) and (f)] at the highest temperature . (a)–(c) correspond to (in gas phase) and (d)–(f) to (in aqueous solution). VMD software (Ref. 86) and RASTER 3D software (Ref. 87) were used to create the figures.

Image of FIG. 14.
FIG. 14.

Time series of the end-to-end distance with (in gas phase) (a) and with (in aqueous solution) (b) at the highest temperature (700 K).

Tables

Generic image for table
Table I.

Acceptance ratios of replica exchanges between pairs of temperatures, , , with fixed from the two-dimensional REM simulation. In the case of , is set to be .

Generic image for table
Table II.

Acceptance ratios of replica exchanges between pairs of parameters, , , with fixed temperatures from the two-dimensional REM simulation. In the case of , is set to be .

Generic image for table
Table III.

Acceptance ratios of -updates, , with fixed in the two-dimensional ST simulation. In the cases of and 8, and are set to be and , respectively.

Generic image for table
Table IV.

Acceptance ratios of -updates, , with fixed in the two-dimensional ST simulation. In the cases of and 4, and are set to be and , respectively.

Generic image for table
Table V.

Differences in the atomistic solvent-accessible surface area and the atomistic solvation free energy of heavy atoms between the lowest-total-energy conformations obtained in aqueous solution and in gas phase [i.e., and ]. We list heavy atoms of N in Ser1, OG in Ser1, OG in Ser2, OD in Asp3, NE in Gln8, OH in Tyr12, NZ in Lys13, OE in Glu16, and OD in Asp17, of which the absolute values of are larger than 1.2 kcal/mol. The solvent-accessible surface area is in and the solvation free energy is in kcal/mol.

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/content/aip/journal/jcp/130/21/10.1063/1.3127783
2009-06-04
2014-04-18
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: Multidimensional generalized-ensemble algorithms for complex systems
http://aip.metastore.ingenta.com/content/aip/journal/jcp/130/21/10.1063/1.3127783
10.1063/1.3127783
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