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Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.

Mashayak SY, Jochum MN, Koschke K, Aluru NR, Rühle V, Junghans C - PLoS ONE (2015)

Bottom Line: We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems.The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations.In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

View Article: PubMed Central - PubMed

Affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America.

ABSTRACT
We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

No MeSH data available.


Comparisons of CG potentials (a) and RDFs (b) for bulk water.All methods fit the target RDF sufficiently well and lead to potential of similar shape. The relative entropy method has a slightly smaller error due the fact that more parameter are available in the potential form.
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pone.0131754.g001: Comparisons of CG potentials (a) and RDFs (b) for bulk water.All methods fit the target RDF sufficiently well and lead to potential of similar shape. The relative entropy method has a slightly smaller error due the fact that more parameter are available in the potential form.

Mentions: Fig 1a shows the optimized CG potentials for bulk water. It can be seen that, although the CG potentials from the relative entropy minimization and simplex are quantitatively different, they exhibit a similar core-softened double-well-type shape, which is a very characterisitc of the water-water CG potential [16, 44].


Relative Entropy and Optimization-Driven Coarse-Graining Methods in VOTCA.

Mashayak SY, Jochum MN, Koschke K, Aluru NR, Rühle V, Junghans C - PLoS ONE (2015)

Comparisons of CG potentials (a) and RDFs (b) for bulk water.All methods fit the target RDF sufficiently well and lead to potential of similar shape. The relative entropy method has a slightly smaller error due the fact that more parameter are available in the potential form.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4507862&req=5

pone.0131754.g001: Comparisons of CG potentials (a) and RDFs (b) for bulk water.All methods fit the target RDF sufficiently well and lead to potential of similar shape. The relative entropy method has a slightly smaller error due the fact that more parameter are available in the potential form.
Mentions: Fig 1a shows the optimized CG potentials for bulk water. It can be seen that, although the CG potentials from the relative entropy minimization and simplex are quantitatively different, they exhibit a similar core-softened double-well-type shape, which is a very characterisitc of the water-water CG potential [16, 44].

Bottom Line: We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems.The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations.In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

View Article: PubMed Central - PubMed

Affiliation: Department of Mechanical Science and Engineering, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, 61801, United States of America.

ABSTRACT
We discuss recent advances of the VOTCA package for systematic coarse-graining. Two methods have been implemented, namely the downhill simplex optimization and the relative entropy minimization. We illustrate the new methods by coarse-graining SPC/E bulk water and more complex water-methanol mixture systems. The CG potentials obtained from both methods are then evaluated by comparing the pair distributions from the coarse-grained to the reference atomistic simulations. In addition to the newly implemented methods, we have also added a parallel analysis framework to improve the computational efficiency of the coarse-graining process.

No MeSH data available.