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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.


Absolute computation time for the radial distribution function calculation as a function of threads.The small system holds 5324, the medium 17687 and the big system 60132 particles. The dashed line shows the ideal scaling line. Also shown are the results from the script-based parallelization of multi_g_rdf.
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pone.0131754.g004: Absolute computation time for the radial distribution function calculation as a function of threads.The small system holds 5324, the medium 17687 and the big system 60132 particles. The dashed line shows the ideal scaling line. Also shown are the results from the script-based parallelization of multi_g_rdf.

Mentions: Fig 4 summarizes the computational times for the calculation of g(r) as a function of the number of threads. It is observed that increasing the number of threads always decreases the total computation time, however, the timings deviate from the ideal scaling line with increasing thread count. Up to 4 threads, the computation time is closer to the ideal scaling, i.e, the parallel speed-up is around 3–4. For 6, 8, and 12 threads, however, the total computation time deviates from the ideal scaling line. The non-ideal time scaling behavior is mainly caused by the constant overhead of the VOTCA input routine and a missing cache optimization. The raw numbers of the computation time for all 960 frames on 1 core are 20s, 68s, and 243s for the small, medium and big system, respectively. For comparison, the GROMACS tool, g_rdf, which is based on simple search, takes 740s, 8116s and 82728s to compute g(r) for the small, medium and big system, respectively. In the former versions of VOTCA, the parallelization of g_rdf was script-based and handled by multi_g_rdf. The trajectory was explicitly split in time into chunks and multiple instances of g_rdf were called. The results for the small and medium systems are also shown in Fig 4.


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)

Absolute computation time for the radial distribution function calculation as a function of threads.The small system holds 5324, the medium 17687 and the big system 60132 particles. The dashed line shows the ideal scaling line. Also shown are the results from the script-based parallelization of multi_g_rdf.
© Copyright Policy
Related In: Results  -  Collection

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

pone.0131754.g004: Absolute computation time for the radial distribution function calculation as a function of threads.The small system holds 5324, the medium 17687 and the big system 60132 particles. The dashed line shows the ideal scaling line. Also shown are the results from the script-based parallelization of multi_g_rdf.
Mentions: Fig 4 summarizes the computational times for the calculation of g(r) as a function of the number of threads. It is observed that increasing the number of threads always decreases the total computation time, however, the timings deviate from the ideal scaling line with increasing thread count. Up to 4 threads, the computation time is closer to the ideal scaling, i.e, the parallel speed-up is around 3–4. For 6, 8, and 12 threads, however, the total computation time deviates from the ideal scaling line. The non-ideal time scaling behavior is mainly caused by the constant overhead of the VOTCA input routine and a missing cache optimization. The raw numbers of the computation time for all 960 frames on 1 core are 20s, 68s, and 243s for the small, medium and big system, respectively. For comparison, the GROMACS tool, g_rdf, which is based on simple search, takes 740s, 8116s and 82728s to compute g(r) for the small, medium and big system, respectively. In the former versions of VOTCA, the parallelization of g_rdf was script-based and handled by multi_g_rdf. The trajectory was explicitly split in time into chunks and multiple instances of g_rdf were called. The results for the small and medium systems are also shown in Fig 4.

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.