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The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials
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10.1063/1.3394863
/content/aip/journal/jcp/132/16/10.1063/1.3394863
http://aip.metastore.ingenta.com/content/aip/journal/jcp/132/16/10.1063/1.3394863

Figures

Image of FIG. 1.
FIG. 1.

Interaction forces between CG water sites with (red) and without (black) three-body potential. Only the results for the COM representation are shown.

Image of FIG. 2.
FIG. 2.

RDF for the one-site CG model for SPC/E water centered in the center of mass of the interacting particle. The use of an explicit three-body CG potential is seen to improve the first shell of solvation greatly.

Image of FIG. 3.
FIG. 3.

RDF for the one-site CG model for SPC/E water centered in the center of geometry of the interacting particle.

Image of FIG. 4.
FIG. 4.

The ADF for SPC/E water computed inside the cutoff of the three-body CG potential for the case with the center of mass CG representation. The three-body potential is seen to closely reproduce the atomistic distribution.

Image of FIG. 5.
FIG. 5.

The ADF for SPC/E water computed inside the cutoff of the three-body CG potential when the center of geometry CG representation is used.

Image of FIG. 6.
FIG. 6.

Probability distributions as a function of two-body distance and three-body angle for each triplet, calculated from: (a) All-atom configurations; (b) CG configurations from CG simulation with both two and three-body CG potentials. The angle is and the distance is one of the . The probability is calculated for the area , with and . Only the results for the COM representation are shown.

Image of FIG. 7.
FIG. 7.

A comparison of the internal energy between the atomistic and CG systems for SPC/E water. Details of how the comparison was performed can be found in Sec. II. The center of mass case is shown. An analogous plot can be obtained from the case where the geometric center is employed instead. (a) the internal energy is computed using only a two-body CG force field. The red line is an actual CG simulation. The blue line reports the value of the potential energy obtained when the same two-body CG potential is applied to a previous all-atom trajectory in CG resolution. (b) Same as (a), but using a three-body CG potential. (c) The distribution of the data presented in (a). (d) The distribution of the data shown in (b).

Image of FIG. 8.
FIG. 8.

Comparison of the virial component of the pressure between atomistic and CG simulations for SPC/E water. The case of COM is shown. The case with the center of geometric is analogous. (a) The virial is computed using only a two-body CG force field. The red line is an actual CG simulation. The blue line reports the value of the virial obtained when the same two-body CG potential is applied to a previous all-atom trajectory in CG resolution. (b) Same as (a), but using a three-body CG potential. (c) The distribution of the data presented in (a). (d) The distribution of the data shown in (b).

Image of FIG. 9.
FIG. 9.

The virial part of the pressure computed for different densities. The comparison is performed employing the two-body CG potential. For a detailed discussion on how the comparison is performed, see Sec. II D. The curves have the same shape as can be evidenced from shifting the CG simulation data upward (dashed line). The difference is only due to an almost constant shift. Only the center of mass case is shown as the geometric center produces a similar plot.

Image of FIG. 10.
FIG. 10.

Same plot as in Fig. 9 but for systems employing an explicit three-body potential. Now the agreement is closer, even though a constant shift can be still observed.

Tables

Generic image for table
Table I.

Computational efficiency. is the CPU time required to finish the simulation. In the last two columns, this value is normalized with respect to GROMACS’ or LAMMPS’ . For the three-body case the cutoff employed is given in parentheses.

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/content/aip/journal/jcp/132/16/10.1063/1.3394863
2010-04-26
2014-04-24
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: The multiscale coarse-graining method. VI. Implementation of three-body coarse-grained potentials
http://aip.metastore.ingenta.com/content/aip/journal/jcp/132/16/10.1063/1.3394863
10.1063/1.3394863
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