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The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
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10.1063/1.2938857
/content/aip/journal/jcp/128/24/10.1063/1.2938857
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/24/10.1063/1.2938857

Figures

Image of FIG. 1.
FIG. 1.

The RDFs computed from simulations of the atomistic (dashed curve) and MS-CG (solid curve) model of methanol are compared. The difference between the two curves results from the use of basis functions that describe the CG force field as a sum of pairwise additive terms. This small difference indicates that the many-body PMF for the one-site CG model of methanol is well represented by a sum of pair-additive interactions between sites.

Image of FIG. 2.
FIG. 2.

The distribution of the velocities of CG sites in the direction computed from MD simulations of the atomistic (dashed curve) and MS-CG (solid curve) model of methanol.

Image of FIG. 3.
FIG. 3.

The inset presents the pair CG force calculated using the linear spline basis and a conjugate gradient algorithm involving the normal matrix to iteratively minimize the MS-CG residual. This force function provides the most accurate approximation to the many-body PMF obtained in the present calculations. See Table I. The main figure presents the difference between this calculated force and force calculated in various other ways. “Normal” refers to the use of the normal matrix and a conjugate gradient algorithm, whereas “block-averaged” refers to the use of nonsymmetric matrix, a biconjugate gradient algorithm, and the BA approximation. “Delta” refers to the use of the delta function basis, “linear” refers to the use of the linear spline basis, and “cubic” refers to the use of the cubic spline basis representation. All the calculations used approximately the same large number of configurations and so all are subject to approximately the same statistical error. The small differences among the curves for demonstrate that in this case the systematic error in the BA approximation is negligible for the block size used and that the calculated CG force function is insensitive to the basis set used and the algorithm used to minimize the residual.

Image of FIG. 4.
FIG. 4.

The molecular structure of the ion pair is represented with five CG sites. CG sites , , , and describe the cation, while site describes the anion. The coordinates of each site are defined by the center of mass coordinates for the atoms involved in the site.

Image of FIG. 5.
FIG. 5.

Bonded distribution functions calculated from MD simulations of the atomistic (dashed curve) and MS-CG (solid curve) model of the ion pair are presented for (a) the distribution of site bond displacements, (b) the distribution of site valence angles, and (c) the distribution of site dihedral angles.

Image of FIG. 6.
FIG. 6.

Nonbonded RDFs calculated from atomistic (dashed curve) and CG (soli d curve) MD simulations of the ion pair are presented for the distributions of (a) site pairs, (b) site pairs, (c) site pairs, and (d) site pairs.

Image of FIG. 7.
FIG. 7.

Short-ranged nonbonded interactions in the MS-CG force field calculated for the ionic liquid system are presented for (a) site pairs, (b) site pairs, (c) site pairs, and (d) site pairs.

Image of FIG. 8.
FIG. 8.

The analytic functional forms (solid curves) approximating the calculated MS-CG bonded interactions (dashed curves) in CG MD simulations of the ion pair are presented for the (a) the bond interaction, (b) the valence angle interaction, and (c) the dihedral angle interaction.

Tables

Generic image for table
Table I.

Parameters describing calculations using various methods for minimizing the MS-CG residual function to obtain the methanol CG pair force. The total number of parameters, , the magnitude of the MS-CG residual, , and the condition number (both before and after preconditioning) obtained from iteratively minimizing the residual using either the normal matrix (normal) or the nonsymmetric matrix with the block-averaging (BA) approximation are presented for each basis set. The BA result for the cubic spline has been presented for both 980 (b) and 1000 (c) configurations. Poor sampling of the core region in the 99th block introduced statistical error into the BA calculation for the cubic spline basis set resulting in an abnormally high magnitude residual. Every other variational calculation described in the table employed the same 1000 configurations sampled from atomistic MD simulations of the methanol as discussed in the text. In each calculation employing the BA approximation, these 1000 configurations were partitioned into 100 disjoint sets of 10 configurations each, the MS-CG variational calculation was performed with the configurations in the block, and the resulting 100 calculated force curves were averaged.

Generic image for table
Table II.

Parameters describing the CG mapping for the ionic liquid system. The coordinates for each site were defined by the center of mass coordinates for the set of atoms involved in the definition of the site. The mass and charge for each CG site were determined by summing the total masses and charges for the atoms involved in each site.

Generic image for table
Table III.

Parameters describing the bonded MS-CG force field for the ionic liquid system. The bonded MS-CG interactions were determined without assuming any functional forms but were then approximately represented by the analytic functions described above in CG MD simulations with the DḺPOLY program (Ref. 57). The analytic functional form for each interaction and the parameters used in fitting the MS-CG interactions are presented.

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/content/aip/journal/jcp/128/24/10.1063/1.2938857
2008-06-27
2014-04-23
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752b84549af89a08dbdd7fdb8b9568b5 journal.articlezxybnytfddd
Scitation: The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
http://aip.metastore.ingenta.com/content/aip/journal/jcp/128/24/10.1063/1.2938857
10.1063/1.2938857
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