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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.


Related in: MedlinePlus

Comparisons of the CG potentials and RDFs of methanol-water: Mixture at different methanol mole fractions, X = 0.062,0.5,0.938 are shown.Arrow indicates the direction of increasing X. All methods fit the target RDF very well for all mole fractions.
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pone.0131754.g002: Comparisons of the CG potentials and RDFs of methanol-water: Mixture at different methanol mole fractions, X = 0.062,0.5,0.938 are shown.Arrow indicates the direction of increasing X. All methods fit the target RDF very well for all mole fractions.

Mentions: The CG potentials obtained from the simplex optimization and the relative entropy minimization for the three different water-methanol mixtures are shown in Fig 2 along with the corresponding RDFs obtained from the CG simulations. Observations about the accuracies of the CG potentials from the simplex and relative entropy methods are similar to that of the bulk water case. Despite the limited flexibility of the CKDg form, the CG potentials from the simplex optimization are able to predict the RDFs reasonably well. As expected, due to the finely tabulated nature of the CBSPL functional form, the CG potentials from the relative entropy optimization are able to predict the water-water, water-methanol, and methanol-methanol RDFs as accurately as the reference AA simulations. We note that the CG potentials for the water-methanol mixture system are different for different mole-fractions. This is not surprising, because it is well-known that the CG potentials depend on the thermodynamic state of the reference system [8, 9]. However, it is possible to optimize CG potentials for multiple state-points simultaneously [51], but it is beyond the scope of this work.


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 the CG potentials and RDFs of methanol-water: Mixture at different methanol mole fractions, X = 0.062,0.5,0.938 are shown.Arrow indicates the direction of increasing X. All methods fit the target RDF very well for all mole fractions.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131754.g002: Comparisons of the CG potentials and RDFs of methanol-water: Mixture at different methanol mole fractions, X = 0.062,0.5,0.938 are shown.Arrow indicates the direction of increasing X. All methods fit the target RDF very well for all mole fractions.
Mentions: The CG potentials obtained from the simplex optimization and the relative entropy minimization for the three different water-methanol mixtures are shown in Fig 2 along with the corresponding RDFs obtained from the CG simulations. Observations about the accuracies of the CG potentials from the simplex and relative entropy methods are similar to that of the bulk water case. Despite the limited flexibility of the CKDg form, the CG potentials from the simplex optimization are able to predict the RDFs reasonably well. As expected, due to the finely tabulated nature of the CBSPL functional form, the CG potentials from the relative entropy optimization are able to predict the water-water, water-methanol, and methanol-methanol RDFs as accurately as the reference AA simulations. We note that the CG potentials for the water-methanol mixture system are different for different mole-fractions. This is not surprising, because it is well-known that the CG potentials depend on the thermodynamic state of the reference system [8, 9]. However, it is possible to optimize CG potentials for multiple state-points simultaneously [51], but it is beyond the scope of this work.

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.


Related in: MedlinePlus