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The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials
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10.1063/1.3599049
/content/aip/journal/jcp/134/22/10.1063/1.3599049
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/22/10.1063/1.3599049
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Figures

Image of FIG. 1.
FIG. 1.

Methanol-methanol CG PMF at selected temperatures. The PMF results were calculated between the mass centers of two methanol molecules as the CG sites. The approximate error bars in the PMF curves are below 5% of the data values based on the block averages.

Image of FIG. 2.
FIG. 2.

Methanol-methanol CG RDF at selected temperatures. The temperatures are the same as those in Fig. 1. The RDF results were calculated between the mass centers of two methanol molecules as the CG sites.

Image of FIG. 3.
FIG. 3.

Comparing the MS-CG result of the methanol-methanol at 310 K with the conventional two-body PMF result. The approximate error bars in the curves are below 5% of the data values based on block averages.

Image of FIG. 4.
FIG. 4.

Energy-entropy decomposition of the methanol-methanol CG PMF at 310 K. The CG site is on the mass center of the methanol molecule. The approximate error bars in the curves are below 5% of the data values based on the block averages.

Image of FIG. 5.
FIG. 5.

The configuration of a hydrogen-bonded methanol dimer after energy minimization. The two orange beads are the center of mass positions for the two molecules.

Image of FIG. 6.
FIG. 6.

Energy-entropy decomposition of the methanol-methanol CG PMF at 310 K. The CG site is on the carbon atom. The approximate error bars in the curves are below 5% of the data values based on the block averages.

Image of FIG. 7.
FIG. 7.

Energy-entropy decomposition of the methanol-methanol CG PMF at 310 K. The CG site is on the oxygen atom. The approximate error bars in the curves are below 5% of the data values based on the block averages.

Image of FIG. 8.
FIG. 8.

Temperature dependence of the methanol-methanol CG PMF for the two selected inter-molecular distances. The approximate error bars in the curves are below 5% of the data values based on the block averages.

Image of FIG. 9.
FIG. 9.

Results for the energetic and entropic components of the CG PMF, computed from a linear analytical fitting and numerical differentiation, respectively. The linear fitting is based on eleven temperature values from 230 to 330 K. The approximate error bars in the curves are below 5% of the data values based on block averages.

Image of FIG. 10.
FIG. 10.

CG PMF results at selected temperatures, computed from a linear analytical fitting and individual MS-CG calculations, respectively. The linear fitting is based on eleven temperature values from 230 to 330 K. The approximate error bars in the curves are below 5% of the data values based on the block averages.

Image of FIG. 11.
FIG. 11.

Two types of DMPC lipid CG schemes. The CG scheme in (a) contains two beads for the headgroup and another three beads for the linker region. The CG scheme in (b) is simpler, with only one bead for the headgroup and another bead for the linker.

Image of FIG. 12.
FIG. 12.

CG PMF and the energy-entropy decomposition results for selected CG interactions. Black, red, and green curves stand for ΔW(r), ΔE(r), and −TΔS(r), respectively. The results are based on the lipid CG scheme in Fig. 6(a) and implicit CG water. The approximate error bars in the PMF curves are below 5% of the PMF values based on block averages, whereas the corresponding numbers for the energetic and entropic components are 5%–10%.

Image of FIG. 13.
FIG. 13.

The CG PMF and the energy-entropy decomposition results for the interaction between lipid headgroups (HD-HD in Fig. 6(b)). The CG lipid model in Fig. 6(b) was implemented with solvent-free coarse-graining. The approximate error bars in the PMF curves are below 5% of the PMF values based on block averages, whereas the corresponding numbers for the energetic and entropic components are 5%–10%.

Image of FIG. 14.
FIG. 14.

The same CG PMF and the energy-entropy decomposition results as those in Fig. 8, calculated instead with one site CG water. The approximate error bars in the PMF curves are below 5% of the PMF values based on block averages, whereas the corresponding numbers for the energetic and entropic components are 5%–10%.

Image of FIG. 15.
FIG. 15.

The CG PMF for the lipid tail SM-SM interaction. The results are for the simplified lipid model in Fig. 6(b) with solvent-free and one site CG water. The approximate error bars in the PMF curves are below 5% of the PMF values based on block averages.

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/content/aip/journal/jcp/134/22/10.1063/1.3599049
2011-06-14
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials
http://aip.metastore.ingenta.com/content/aip/journal/jcp/134/22/10.1063/1.3599049
10.1063/1.3599049
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